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.
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19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
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41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <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.2.10.2b2">2.10.2b2</a><br />
74 <em>2/10/2017</em></strong>
77 <td><div align="left">
86 <td><div align="left">
96 <td width="60" nowrap>
98 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
99 <em>7/9/2017</em></strong>
102 <td><div align="left">
106 <!-- JAL-2588 -->Show gaps in overview window by colouring
107 in grey (sequences used to be coloured grey, and gaps were
111 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
115 <!-- JAL-2587 -->Overview updates immediately on increase
116 in size and progress bar shown as higher resolution
117 overview is recalculated
122 <td><div align="left">
126 <!-- JAL-2664 -->Overview window redraws every hidden
127 column region row by row
130 <!-- JAL-2681 -->duplicate protein sequences shown after
131 retrieving Ensembl crossrefs for sequences from Uniprot
134 <!-- JAL-2603 -->Overview window throws NPE if show boxes
135 format setting is unticked
138 <!-- JAL-2610 -->Groups are coloured wrongly in overview
139 if group has show boxes format setting unticked
142 <!-- JAL-2672,JAL-2665 -->Redraw problems when
143 autoscrolling whilst dragging current selection group to
144 include sequences and columns not currently displayed
147 <!-- JAL-2691 -->Not all chains are mapped when multimeric
148 assemblies are imported via CIF file
151 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
152 displayed when threshold or conservation colouring is also
156 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
160 <!-- JAL-2673 -->Jalview continues to scroll after
161 dragging a selected region off the visible region of the
165 <!-- JAL-2724 -->Cannot apply annotation based
166 colourscheme to all groups in a view
169 <!-- JAL-2511 -->IDs don't line up with sequences
170 initially after font size change using the Font chooser or
177 <td width="60" nowrap>
179 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
182 <td><div align="left">
183 <em>Calculations</em>
187 <!-- JAL-1933 -->Occupancy annotation row shows number of
188 ungapped positions in each column of the alignment.
191 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
192 a calculation dialog box
195 <!-- JAL-2379 -->Revised implementation of PCA for speed
196 and memory efficiency (~30x faster)
199 <!-- JAL-2403 -->Revised implementation of sequence
200 similarity scores as used by Tree, PCA, Shading Consensus
201 and other calculations
204 <!-- JAL-2416 -->Score matrices are stored as resource
205 files within the Jalview codebase
208 <!-- JAL-2500 -->Trees computed on Sequence Feature
209 Similarity may have different topology due to increased
216 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
217 model for alignments and groups
220 <!-- JAL-384 -->Custom shading schemes created via groovy
227 <!-- JAL-2526 -->Efficiency improvements for interacting
228 with alignment and overview windows
231 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
235 <!-- JAL-2388 -->Hidden columns and sequences can be
239 <!-- JAL-2611 -->Click-drag in visible area allows fine
240 adjustment of visible position
244 <em>Data import/export</em>
247 <!-- JAL-2535 -->Posterior probability annotation from
248 Stockholm files imported as sequence associated annotation
251 <!-- JAL-2507 -->More robust per-sequence positional
252 annotation input/output via stockholm flatfile
255 <!-- JAL-2533 -->Sequence names don't include file
256 extension when importing structure files without embedded
257 names or PDB accessions
260 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
261 format sequence substitution matrices
264 <em>User Interface</em>
267 <!-- JAL-2447 --> Experimental Features Checkbox in
268 Desktop's Tools menu to hide or show untested features in
272 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
273 via Overview or sequence motif search operations
276 <!-- JAL-2547 -->Amend sequence features dialog box can be
277 opened by double clicking gaps within sequence feature
281 <!-- JAL-1476 -->Status bar message shown when not enough
282 aligned positions were available to create a 3D structure
286 <em>3D Structure</em>
289 <!-- JAL-2430 -->Hidden regions in alignment views are not
290 coloured in linked structure views
293 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
294 file-based command exchange
297 <!-- JAL-2375 -->Structure chooser automatically shows
298 Cached Structures rather than querying the PDBe if
299 structures are already available for sequences
302 <!-- JAL-2520 -->Structures imported via URL are cached in
303 the Jalview project rather than downloaded again when the
307 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
308 to transfer Chimera's structure attributes as Jalview
309 features, and vice-versa (<strong>Experimental
313 <em>Web Services</em>
316 <!-- JAL-2549 -->Updated JABAWS client to v2.2
319 <!-- JAL-2335 -->Filter non-standard amino acids and
320 nucleotides when submitting to AACon and other MSA
324 <!-- JAL-2316, -->URLs for viewing database
325 cross-references provided by identifiers.org and the
333 <!-- JAL-2344 -->FileFormatI interface for describing and
334 identifying file formats (instead of String constants)
337 <!-- JAL-2228 -->FeatureCounter script refactored for
338 efficiency when counting all displayed features (not
339 backwards compatible with 2.10.1)
342 <em>Example files</em>
345 <!-- JAL-2631 -->Graduated feature colour style example
346 included in the example feature file
349 <em>Documentation</em>
352 <!-- JAL-2339 -->Release notes reformatted for readability
353 with the built-in Java help viewer
356 <!-- JAL-1644 -->Find documentation updated with 'search
357 sequence description' option
363 <!-- JAL-2485, -->External service integration tests for
364 Uniprot REST Free Text Search Client
367 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
370 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
375 <td><div align="left">
376 <em>Calculations</em>
379 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
380 matrix - C->R should be '-3'<br />Old matrix restored
381 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
383 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
384 Jalview's treatment of gaps in PCA and substitution matrix
385 based Tree calculations.<br /> <br />In earlier versions
386 of Jalview, gaps matching gaps were penalised, and gaps
387 matching non-gaps penalised even more. In the PCA
388 calculation, gaps were actually treated as non-gaps - so
389 different costs were applied, which meant Jalview's PCAs
390 were different to those produced by SeqSpace.<br />Jalview
391 now treats gaps in the same way as SeqSpace (ie it scores
392 them as 0). <br /> <br />Enter the following in the
393 Groovy console to restore pre-2.10.2 behaviour:<br />
394 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
395 // for 2.10.1 mode <br />
396 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
397 // to restore 2.10.2 mode <br /> <br /> <em>Note:
398 these settings will affect all subsequent tree and PCA
399 calculations (not recommended)</em></li>
401 <!-- JAL-2424 -->Fixed off-by-one bug that affected
402 scaling of branch lengths for trees computed using
403 Sequence Feature Similarity.
406 <!-- JAL-2377 -->PCA calculation could hang when
407 generating output report when working with highly
411 <!-- JAL-2544 --> Sort by features includes features to
412 right of selected region when gaps present on right-hand
416 <em>User Interface</em>
419 <!-- JAL-2346 -->Reopening Colour by annotation dialog
420 doesn't reselect a specific sequence's associated
421 annotation after it was used for colouring a view
424 <!-- JAL-2419 -->Current selection lost if popup menu
425 opened on a region of alignment without groups
428 <!-- JAL-2374 -->Popup menu not always shown for regions
429 of an alignment with overlapping groups
432 <!-- JAL-2310 -->Finder double counts if both a sequence's
433 name and description match
436 <!-- JAL-2370 -->Hiding column selection containing two
437 hidden regions results in incorrect hidden regions
440 <!-- JAL-2386 -->'Apply to all groups' setting when
441 changing colour does not apply Conservation slider value
445 <!-- JAL-2373 -->Percentage identity and conservation menu
446 items do not show a tick or allow shading to be disabled
449 <!-- JAL-2385 -->Conservation shading or PID threshold
450 lost when base colourscheme changed if slider not visible
453 <!-- JAL-2547 -->Sequence features shown in tooltip for
454 gaps before start of features
457 <!-- JAL-2623 -->Graduated feature colour threshold not
458 restored to UI when feature colour is edited
461 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
462 a time when scrolling vertically in wrapped mode.
465 <!-- JAL-2630 -->Structure and alignment overview update
466 as graduate feature colour settings are modified via the
470 <!-- JAL-2034 -->Overview window doesn't always update
471 when a group defined on the alignment is resized
474 <!-- JAL-2605 -->Mouseovers on left/right scale region in
475 wrapped view result in positional status updates
479 <!-- JAL-2563 -->Status bar doesn't show position for
480 ambiguous amino acid and nucleotide symbols
483 <!-- JAL-2602 -->Copy consensus sequence failed if
484 alignment included gapped columns
487 <!-- JAL-2473 -->Minimum size set for Jalview windows so
488 widgets don't permanently disappear
491 <!-- JAL-2503 -->Cannot select or filter quantitative
492 annotation that are shown only as column labels (e.g.
493 T-Coffee column reliability scores)
496 <!-- JAL-2594 -->Exception thrown if trying to create a
497 sequence feature on gaps only
500 <!-- JAL-2504 -->Features created with 'New feature'
501 button from a Find inherit previously defined feature type
502 rather than the Find query string
505 <!-- JAL-2423 -->incorrect title in output window when
506 exporting tree calculated in Jalview
509 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
510 and then revealing them reorders sequences on the
514 <!-- JAL-964 -->Group panel in sequence feature settings
515 doesn't update to reflect available set of groups after
516 interactively adding or modifying features
519 <!-- JAL-2225 -->Sequence Database chooser unusable on
523 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
524 only excluded gaps in current sequence and ignored
531 <!-- JAL-2421 -->Overview window visible region moves
532 erratically when hidden rows or columns are present
535 <!-- JAL-2362 -->Per-residue colourschemes applied via the
536 Structure Viewer's colour menu don't correspond to
540 <!-- JAL-2405 -->Protein specific colours only offered in
541 colour and group colour menu for protein alignments
544 <!-- JAL-2385 -->Colour threshold slider doesn't update to
545 reflect currently selected view or group's shading
549 <!-- JAL-2624 -->Feature colour thresholds not respected
550 when rendered on overview and structures when opacity at
554 <!-- JAL-2589 -->User defined gap colour not shown in
555 overview when features overlaid on alignment
558 <em>Data import/export</em>
561 <!-- JAL-2576 -->Very large alignments take a long time to
565 <!-- JAL-2507 -->Per-sequence RNA secondary structures
566 added after a sequence was imported are not written to
570 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
571 when importing RNA secondary structure via Stockholm
574 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
575 not shown in correct direction for simple pseudoknots
578 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
579 with lightGray or darkGray via features file (but can
583 <!-- JAL-2383 -->Above PID colour threshold not recovered
584 when alignment view imported from project
587 <!-- JAL-2520,JAL-2465 -->No mappings generated between
588 structure and sequences extracted from structure files
589 imported via URL and viewed in Jmol
592 <!-- JAL-2520 -->Structures loaded via URL are saved in
593 Jalview Projects rather than fetched via URL again when
594 the project is loaded and the structure viewed
597 <em>Web Services</em>
600 <!-- JAL-2519 -->EnsemblGenomes example failing after
601 release of Ensembl v.88
604 <!-- JAL-2366 -->Proxy server address and port always
605 appear enabled in Preferences->Connections
608 <!-- JAL-2461 -->DAS registry not found exceptions
609 removed from console output
612 <!-- JAL-2582 -->Cannot retrieve protein products from
613 Ensembl by Peptide ID
616 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
617 created from SIFTs, and spurious 'Couldn't open structure
618 in Chimera' errors raised after April 2017 update (problem
619 due to 'null' string rather than empty string used for
620 residues with no corresponding PDB mapping).
623 <em>Application UI</em>
626 <!-- JAL-2361 -->User Defined Colours not added to Colour
630 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
631 case' residues (button in colourscheme editor debugged and
632 new documentation and tooltips added)
635 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
636 doesn't restore group-specific text colour thresholds
639 <!-- JAL-2243 -->Feature settings panel does not update as
640 new features are added to alignment
643 <!-- JAL-2532 -->Cancel in feature settings reverts
644 changes to feature colours via the Amend features dialog
647 <!-- JAL-2506 -->Null pointer exception when attempting to
648 edit graduated feature colour via amend features dialog
652 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
653 selection menu changes colours of alignment views
656 <!-- JAL-2426 -->Spurious exceptions in console raised
657 from alignment calculation workers after alignment has
661 <!-- JAL-1608 -->Typo in selection popup menu - Create
662 groups now 'Create Group'
665 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
666 Create/Undefine group doesn't always work
669 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
670 shown again after pressing 'Cancel'
673 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
674 adjusts start position in wrap mode
677 <!-- JAL-2563 -->Status bar doesn't show positions for
678 ambiguous amino acids
681 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
682 CDS/Protein view after CDS sequences added for aligned
686 <!-- JAL-2592 -->User defined colourschemes called 'User
687 Defined' don't appear in Colours menu
693 <!-- JAL-2468 -->Switching between Nucleotide and Protein
694 score models doesn't always result in an updated PCA plot
697 <!-- JAL-2442 -->Features not rendered as transparent on
698 overview or linked structure view
701 <!-- JAL-2372 -->Colour group by conservation doesn't
705 <!-- JAL-2517 -->Hitting Cancel after applying
706 user-defined colourscheme doesn't restore original
713 <!-- JAL-2314 -->Unit test failure:
714 jalview.ws.jabaws.RNAStructExportImport setup fails
717 <!-- JAL-2307 -->Unit test failure:
718 jalview.ws.sifts.SiftsClientTest due to compatibility
719 problems with deep array comparison equality asserts in
720 successive versions of TestNG
723 <!-- JAL-2479 -->Relocated StructureChooserTest and
724 ParameterUtilsTest Unit tests to Network suite
727 <em>New Known Issues</em>
730 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
731 phase after a sequence motif find operation
734 <!-- JAL-2550 -->Importing annotation file with rows
735 containing just upper and lower case letters are
736 interpreted as WUSS RNA secondary structure symbols
739 <!-- JAL-2590 -->Cannot load and display Newick trees
740 reliably from eggnog Ortholog database
743 <!-- JAL-2468 -->Status bar shows 'Marked x columns
744 containing features of type Highlight' when 'B' is pressed
745 to mark columns containing highlighted regions.
748 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
749 doesn't always add secondary structure annotation.
754 <td width="60" nowrap>
756 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
759 <td><div align="left">
763 <!-- JAL-98 -->Improved memory usage: sparse arrays used
764 for all consensus calculations
767 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
770 <li>Updated Jalview's Certum code signing certificate
776 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
777 set of database cross-references, sorted alphabetically
780 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
781 from database cross references. Users with custom links
782 will receive a <a href="webServices/urllinks.html#warning">warning
783 dialog</a> asking them to update their preferences.
786 <!-- JAL-2287-->Cancel button and escape listener on
787 dialog warning user about disconnecting Jalview from a
791 <!-- JAL-2320-->Jalview's Chimera control window closes if
792 the Chimera it is connected to is shut down
795 <!-- JAL-1738-->New keystroke (B) and Select highlighted
796 columns menu item to mark columns containing highlighted
797 regions (e.g. from structure selections or results of a
801 <!-- JAL-2284-->Command line option for batch-generation
802 of HTML pages rendering alignment data with the BioJS
812 <!-- JAL-2286 -->Columns with more than one modal residue
813 are not coloured or thresholded according to percent
814 identity (first observed in Jalview 2.8.2)
817 <!-- JAL-2301 -->Threonine incorrectly reported as not
821 <!-- JAL-2318 -->Updates to documentation pages (above PID
822 threshold, amino acid properties)
825 <!-- JAL-2292 -->Lower case residues in sequences are not
826 reported as mapped to residues in a structure file in the
830 <!--JAL-2324 -->Identical features with non-numeric scores
831 could be added multiple times to a sequence
834 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
835 bond features shown as two highlighted residues rather
836 than a range in linked structure views, and treated
837 correctly when selecting and computing trees from features
840 <!-- JAL-2281-->Custom URL links for database
841 cross-references are matched to database name regardless
849 <!-- JAL-2282-->Custom URL links for specific database
850 names without regular expressions also offer links from
854 <!-- JAL-2315-->Removing a single configured link in the
855 URL links pane in Connections preferences doesn't actually
856 update Jalview configuration
859 <!-- JAL-2272-->CTRL-Click on a selected region to open
860 the alignment area popup menu doesn't work on El-Capitan
863 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
864 files with similarly named sequences if dropped onto the
868 <!-- JAL-2312 -->Additional mappings are shown for PDB
869 entries where more chains exist in the PDB accession than
870 are reported in the SIFTS file
873 <!-- JAL-2317-->Certain structures do not get mapped to
874 the structure view when displayed with Chimera
877 <!-- JAL-2317-->No chains shown in the Chimera view
878 panel's View->Show Chains submenu
881 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
882 work for wrapped alignment views
885 <!--JAL-2197 -->Rename UI components for running JPred
886 predictions from 'JNet' to 'JPred'
889 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
890 corrupted when annotation panel vertical scroll is not at
894 <!--JAL-2332 -->Attempting to view structure for Hen
895 lysozyme results in a PDB Client error dialog box
898 <!-- JAL-2319 -->Structure View's mapping report switched
899 ranges for PDB and sequence for SIFTS
902 SIFTS 'Not_Observed' residues mapped to non-existant
906 <!-- <em>New Known Issues</em>
913 <td width="60" nowrap>
915 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
916 <em>25/10/2016</em></strong>
919 <td><em>Application</em>
921 <li>3D Structure chooser opens with 'Cached structures'
922 view if structures already loaded</li>
923 <li>Progress bar reports models as they are loaded to
930 <li>Colour by conservation always enabled and no tick
931 shown in menu when BLOSUM or PID shading applied</li>
932 <li>FER1_ARATH and FER2_ARATH labels were switched in
933 example sequences/projects/trees</li>
937 <li>Jalview projects with views of local PDB structure
938 files saved on Windows cannot be opened on OSX</li>
939 <li>Multiple structure views can be opened and superposed
940 without timeout for structures with multiple models or
941 multiple sequences in alignment</li>
942 <li>Cannot import or associated local PDB files without a
943 PDB ID HEADER line</li>
944 <li>RMSD is not output in Jmol console when superposition
946 <li>Drag and drop of URL from Browser fails for Linux and
947 OSX versions earlier than El Capitan</li>
948 <li>ENA client ignores invalid content from ENA server</li>
949 <li>Exceptions are not raised in console when ENA client
950 attempts to fetch non-existent IDs via Fetch DB Refs UI
952 <li>Exceptions are not raised in console when a new view
953 is created on the alignment</li>
954 <li>OSX right-click fixed for group selections: CMD-click
955 to insert/remove gaps in groups and CTRL-click to open group
958 <em>Build and deployment</em>
960 <li>URL link checker now copes with multi-line anchor
963 <em>New Known Issues</em>
965 <li>Drag and drop from URL links in browsers do not work
972 <td width="60" nowrap>
974 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
980 <!-- JAL-2124 -->Updated Spanish translations.
983 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
984 for importing structure data to Jalview. Enables mmCIF and
988 <!-- JAL-192 --->Alignment ruler shows positions relative to
992 <!-- JAL-2202 -->Position/residue shown in status bar when
993 mousing over sequence associated annotation
996 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
1000 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1001 '()', canonical '[]' and invalid '{}' base pair populations
1005 <!-- JAL-2092 -->Feature settings popup menu options for
1006 showing or hiding columns containing a feature
1009 <!-- JAL-1557 -->Edit selected group by double clicking on
1010 group and sequence associated annotation labels
1013 <!-- JAL-2236 -->Sequence name added to annotation label in
1014 select/hide columns by annotation and colour by annotation
1018 </ul> <em>Application</em>
1021 <!-- JAL-2050-->Automatically hide introns when opening a
1022 gene/transcript view
1025 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1029 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1030 structure mappings with the EMBL-EBI PDBe SIFTS database
1033 <!-- JAL-2079 -->Updated download sites used for Rfam and
1034 Pfam sources to xfam.org
1037 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1040 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1041 over sequences in Jalview
1044 <!-- JAL-2027-->Support for reverse-complement coding
1045 regions in ENA and EMBL
1048 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1049 for record retrieval via ENA rest API
1052 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1056 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1057 groovy script execution
1060 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1061 alignment window's Calculate menu
1064 <!-- JAL-1812 -->Allow groovy scripts that call
1065 Jalview.getAlignFrames() to run in headless mode
1068 <!-- JAL-2068 -->Support for creating new alignment
1069 calculation workers from groovy scripts
1072 <!-- JAL-1369 --->Store/restore reference sequence in
1076 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1077 associations are now saved/restored from project
1080 <!-- JAL-1993 -->Database selection dialog always shown
1081 before sequence fetcher is opened
1084 <!-- JAL-2183 -->Double click on an entry in Jalview's
1085 database chooser opens a sequence fetcher
1088 <!-- JAL-1563 -->Free-text search client for UniProt using
1089 the UniProt REST API
1092 <!-- JAL-2168 -->-nonews command line parameter to prevent
1093 the news reader opening
1096 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1097 querying stored in preferences
1100 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1104 <!-- JAL-1977-->Tooltips shown on database chooser
1107 <!-- JAL-391 -->Reverse complement function in calculate
1108 menu for nucleotide sequences
1111 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1112 and feature counts preserves alignment ordering (and
1113 debugged for complex feature sets).
1116 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1117 viewing structures with Jalview 2.10
1120 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1121 genome, transcript CCDS and gene ids via the Ensembl and
1122 Ensembl Genomes REST API
1125 <!-- JAL-2049 -->Protein sequence variant annotation
1126 computed for 'sequence_variant' annotation on CDS regions
1130 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1134 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1135 Ref Fetcher fails to match, or otherwise updates sequence
1136 data from external database records.
1139 <!-- JAL-2154 -->Revised Jalview Project format for
1140 efficient recovery of sequence coding and alignment
1141 annotation relationships.
1143 </ul> <!-- <em>Applet</em>
1154 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1158 <!-- JAL-2018-->Export features in Jalview format (again)
1159 includes graduated colourschemes
1162 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1163 working with big alignments and lots of hidden columns
1166 <!-- JAL-2053-->Hidden column markers not always rendered
1167 at right of alignment window
1170 <!-- JAL-2067 -->Tidied up links in help file table of
1174 <!-- JAL-2072 -->Feature based tree calculation not shown
1178 <!-- JAL-2075 -->Hidden columns ignored during feature
1179 based tree calculation
1182 <!-- JAL-2065 -->Alignment view stops updating when show
1183 unconserved enabled for group on alignment
1186 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1190 <!-- JAL-2146 -->Alignment column in status incorrectly
1191 shown as "Sequence position" when mousing over
1195 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1196 hidden columns present
1199 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1200 user created annotation added to alignment
1203 <!-- JAL-1841 -->RNA Structure consensus only computed for
1204 '()' base pair annotation
1207 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1208 in zero scores for all base pairs in RNA Structure
1212 <!-- JAL-2174-->Extend selection with columns containing
1216 <!-- JAL-2275 -->Pfam format writer puts extra space at
1217 beginning of sequence
1220 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1224 <!-- JAL-2238 -->Cannot create groups on an alignment from
1225 from a tree when t-coffee scores are shown
1228 <!-- JAL-1836,1967 -->Cannot import and view PDB
1229 structures with chains containing negative resnums (4q4h)
1232 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1236 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1237 to Clustal, PIR and PileUp output
1240 <!-- JAL-2008 -->Reordering sequence features that are
1241 not visible causes alignment window to repaint
1244 <!-- JAL-2006 -->Threshold sliders don't work in
1245 graduated colour and colour by annotation row for e-value
1246 scores associated with features and annotation rows
1249 <!-- JAL-1797 -->amino acid physicochemical conservation
1250 calculation should be case independent
1253 <!-- JAL-2173 -->Remove annotation also updates hidden
1257 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1258 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1259 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1262 <!-- JAL-2065 -->Null pointer exceptions and redraw
1263 problems when reference sequence defined and 'show
1264 non-conserved' enabled
1267 <!-- JAL-1306 -->Quality and Conservation are now shown on
1268 load even when Consensus calculation is disabled
1271 <!-- JAL-1932 -->Remove right on penultimate column of
1272 alignment does nothing
1275 <em>Application</em>
1278 <!-- JAL-1552-->URLs and links can't be imported by
1279 drag'n'drop on OSX when launched via webstart (note - not
1280 yet fixed for El Capitan)
1283 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1284 output when running on non-gb/us i18n platforms
1287 <!-- JAL-1944 -->Error thrown when exporting a view with
1288 hidden sequences as flat-file alignment
1291 <!-- JAL-2030-->InstallAnywhere distribution fails when
1295 <!-- JAL-2080-->Jalview very slow to launch via webstart
1296 (also hotfix for 2.9.0b2)
1299 <!-- JAL-2085 -->Cannot save project when view has a
1300 reference sequence defined
1303 <!-- JAL-1011 -->Columns are suddenly selected in other
1304 alignments and views when revealing hidden columns
1307 <!-- JAL-1989 -->Hide columns not mirrored in complement
1308 view in a cDNA/Protein splitframe
1311 <!-- JAL-1369 -->Cannot save/restore representative
1312 sequence from project when only one sequence is
1316 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1317 in Structure Chooser
1320 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1321 structure consensus didn't refresh annotation panel
1324 <!-- JAL-1962 -->View mapping in structure view shows
1325 mappings between sequence and all chains in a PDB file
1328 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1329 dialogs format columns correctly, don't display array
1330 data, sort columns according to type
1333 <!-- JAL-1975 -->Export complete shown after destination
1334 file chooser is cancelled during an image export
1337 <!-- JAL-2025 -->Error when querying PDB Service with
1338 sequence name containing special characters
1341 <!-- JAL-2024 -->Manual PDB structure querying should be
1345 <!-- JAL-2104 -->Large tooltips with broken HTML
1346 formatting don't wrap
1349 <!-- JAL-1128 -->Figures exported from wrapped view are
1350 truncated so L looks like I in consensus annotation
1353 <!-- JAL-2003 -->Export features should only export the
1354 currently displayed features for the current selection or
1358 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1359 after fetching cross-references, and restoring from
1363 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1364 followed in the structure viewer
1367 <!-- JAL-2163 -->Titles for individual alignments in
1368 splitframe not restored from project
1371 <!-- JAL-2145 -->missing autocalculated annotation at
1372 trailing end of protein alignment in transcript/product
1373 splitview when pad-gaps not enabled by default
1376 <!-- JAL-1797 -->amino acid physicochemical conservation
1380 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1381 article has been read (reopened issue due to
1382 internationalisation problems)
1385 <!-- JAL-1960 -->Only offer PDB structures in structure
1386 viewer based on sequence name, PDB and UniProt
1391 <!-- JAL-1976 -->No progress bar shown during export of
1395 <!-- JAL-2213 -->Structures not always superimposed after
1396 multiple structures are shown for one or more sequences.
1399 <!-- JAL-1370 -->Reference sequence characters should not
1400 be replaced with '.' when 'Show unconserved' format option
1404 <!-- JAL-1823 -->Cannot specify chain code when entering
1405 specific PDB id for sequence
1408 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1409 'Export hidden sequences' is enabled, but 'export hidden
1410 columns' is disabled.
1413 <!--JAL-2026-->Best Quality option in structure chooser
1414 selects lowest rather than highest resolution structures
1418 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1419 to sequence mapping in 'View Mappings' report
1422 <!-- JAL-2284 -->Unable to read old Jalview projects that
1423 contain non-XML data added after Jalvew wrote project.
1426 <!-- JAL-2118 -->Newly created annotation row reorders
1427 after clicking on it to create new annotation for a
1430 <!-- may exclude, this is an external service stability issue JAL-1941
1431 -- > RNA 3D structure not added via DSSR service</li> -->
1436 <!-- JAL-2151 -->Incorrect columns are selected when
1437 hidden columns present before start of sequence
1440 <!-- JAL-1986 -->Missing dependencies on applet pages
1444 <!-- JAL-1947 -->Overview pixel size changes when
1445 sequences are hidden in applet
1448 <!-- JAL-1996 -->Updated instructions for applet
1449 deployment on examples pages.
1456 <td width="60" nowrap>
1457 <div align="center">
1458 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1459 <em>16/10/2015</em></strong>
1462 <td><em>General</em>
1464 <li>Time stamps for signed Jalview application and applet
1469 <em>Application</em>
1471 <li>Duplicate group consensus and conservation rows
1472 shown when tree is partitioned</li>
1473 <li>Erratic behaviour when tree partitions made with
1474 multiple cDNA/Protein split views</li>
1480 <td width="60" nowrap>
1481 <div align="center">
1482 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1483 <em>8/10/2015</em></strong>
1486 <td><em>General</em>
1488 <li>Updated Spanish translations of localized text for
1490 </ul> <em>Application</em>
1492 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1493 <li>Signed OSX InstallAnywhere installer<br></li>
1494 <li>Support for per-sequence based annotations in BioJSON</li>
1495 </ul> <em>Applet</em>
1497 <li>Split frame example added to applet examples page</li>
1498 </ul> <em>Build and Deployment</em>
1501 <!-- JAL-1888 -->New ant target for running Jalview's test
1509 <li>Mapping of cDNA to protein in split frames
1510 incorrect when sequence start > 1</li>
1511 <li>Broken images in filter column by annotation dialog
1513 <li>Feature colours not parsed from features file</li>
1514 <li>Exceptions and incomplete link URLs recovered when
1515 loading a features file containing HTML tags in feature
1519 <em>Application</em>
1521 <li>Annotations corrupted after BioJS export and
1523 <li>Incorrect sequence limits after Fetch DB References
1524 with 'trim retrieved sequences'</li>
1525 <li>Incorrect warning about deleting all data when
1526 deleting selected columns</li>
1527 <li>Patch to build system for shipping properly signed
1528 JNLP templates for webstart launch</li>
1529 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1530 unreleased structures for download or viewing</li>
1531 <li>Tab/space/return keystroke operation of EMBL-PDBe
1532 fetcher/viewer dialogs works correctly</li>
1533 <li>Disabled 'minimise' button on Jalview windows
1534 running on OSX to workaround redraw hang bug</li>
1535 <li>Split cDNA/Protein view position and geometry not
1536 recovered from jalview project</li>
1537 <li>Initial enabled/disabled state of annotation menu
1538 sorter 'show autocalculated first/last' corresponds to
1540 <li>Restoring of Clustal, RNA Helices and T-Coffee
1541 color schemes from BioJSON</li>
1545 <li>Reorder sequences mirrored in cDNA/Protein split
1547 <li>Applet with Jmol examples not loading correctly</li>
1553 <td><div align="center">
1554 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1556 <td><em>General</em>
1558 <li>Linked visualisation and analysis of DNA and Protein
1561 <li>Translated cDNA alignments shown as split protein
1562 and DNA alignment views</li>
1563 <li>Codon consensus annotation for linked protein and
1564 cDNA alignment views</li>
1565 <li>Link cDNA or Protein product sequences by loading
1566 them onto Protein or cDNA alignments</li>
1567 <li>Reconstruct linked cDNA alignment from aligned
1568 protein sequences</li>
1571 <li>Jmol integration updated to Jmol v14.2.14</li>
1572 <li>Import and export of Jalview alignment views as <a
1573 href="features/bioJsonFormat.html">BioJSON</a></li>
1574 <li>New alignment annotation file statements for
1575 reference sequences and marking hidden columns</li>
1576 <li>Reference sequence based alignment shading to
1577 highlight variation</li>
1578 <li>Select or hide columns according to alignment
1580 <li>Find option for locating sequences by description</li>
1581 <li>Conserved physicochemical properties shown in amino
1582 acid conservation row</li>
1583 <li>Alignments can be sorted by number of RNA helices</li>
1584 </ul> <em>Application</em>
1586 <li>New cDNA/Protein analysis capabilities
1588 <li>Get Cross-References should open a Split Frame
1589 view with cDNA/Protein</li>
1590 <li>Detect when nucleotide sequences and protein
1591 sequences are placed in the same alignment</li>
1592 <li>Split cDNA/Protein views are saved in Jalview
1597 <li>Use REST API to talk to Chimera</li>
1598 <li>Selected regions in Chimera are highlighted in linked
1599 Jalview windows</li>
1601 <li>VARNA RNA viewer updated to v3.93</li>
1602 <li>VARNA views are saved in Jalview Projects</li>
1603 <li>Pseudoknots displayed as Jalview RNA annotation can
1604 be shown in VARNA</li>
1606 <li>Make groups for selection uses marked columns as well
1607 as the active selected region</li>
1609 <li>Calculate UPGMA and NJ trees using sequence feature
1611 <li>New Export options
1613 <li>New Export Settings dialog to control hidden
1614 region export in flat file generation</li>
1616 <li>Export alignment views for display with the <a
1617 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1619 <li>Export scrollable SVG in HTML page</li>
1620 <li>Optional embedding of BioJSON data when exporting
1621 alignment figures to HTML</li>
1623 <li>3D structure retrieval and display
1625 <li>Free text and structured queries with the PDBe
1627 <li>PDBe Search API based discovery and selection of
1628 PDB structures for a sequence set</li>
1632 <li>JPred4 employed for protein secondary structure
1634 <li>Hide Insertions menu option to hide unaligned columns
1635 for one or a group of sequences</li>
1636 <li>Automatically hide insertions in alignments imported
1637 from the JPred4 web server</li>
1638 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1639 system on OSX<br />LGPL libraries courtesy of <a
1640 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1642 <li>changed 'View nucleotide structure' submenu to 'View
1643 VARNA 2D Structure'</li>
1644 <li>change "View protein structure" menu option to "3D
1647 </ul> <em>Applet</em>
1649 <li>New layout for applet example pages</li>
1650 <li>New parameters to enable SplitFrame view
1651 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1652 <li>New example demonstrating linked viewing of cDNA and
1653 Protein alignments</li>
1654 </ul> <em>Development and deployment</em>
1656 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1657 <li>Include installation type and git revision in build
1658 properties and console log output</li>
1659 <li>Jalview Github organisation, and new github site for
1660 storing BioJsMSA Templates</li>
1661 <li>Jalview's unit tests now managed with TestNG</li>
1664 <!-- <em>General</em>
1666 </ul> --> <!-- issues resolved --> <em>Application</em>
1668 <li>Escape should close any open find dialogs</li>
1669 <li>Typo in select-by-features status report</li>
1670 <li>Consensus RNA secondary secondary structure
1671 predictions are not highlighted in amber</li>
1672 <li>Missing gap character in v2.7 example file means
1673 alignment appears unaligned when pad-gaps is not enabled</li>
1674 <li>First switch to RNA Helices colouring doesn't colour
1675 associated structure views</li>
1676 <li>ID width preference option is greyed out when auto
1677 width checkbox not enabled</li>
1678 <li>Stopped a warning dialog from being shown when
1679 creating user defined colours</li>
1680 <li>'View Mapping' in structure viewer shows sequence
1681 mappings for just that viewer's sequences</li>
1682 <li>Workaround for superposing PDB files containing
1683 multiple models in Chimera</li>
1684 <li>Report sequence position in status bar when hovering
1685 over Jmol structure</li>
1686 <li>Cannot output gaps as '.' symbols with Selection ->
1687 output to text box</li>
1688 <li>Flat file exports of alignments with hidden columns
1689 have incorrect sequence start/end</li>
1690 <li>'Aligning' a second chain to a Chimera structure from
1692 <li>Colour schemes applied to structure viewers don't
1693 work for nucleotide</li>
1694 <li>Loading/cut'n'pasting an empty or invalid file leads
1695 to a grey/invisible alignment window</li>
1696 <li>Exported Jpred annotation from a sequence region
1697 imports to different position</li>
1698 <li>Space at beginning of sequence feature tooltips shown
1699 on some platforms</li>
1700 <li>Chimera viewer 'View | Show Chain' menu is not
1702 <li>'New View' fails with a Null Pointer Exception in
1703 console if Chimera has been opened</li>
1704 <li>Mouseover to Chimera not working</li>
1705 <li>Miscellaneous ENA XML feature qualifiers not
1707 <li>NPE in annotation renderer after 'Extract Scores'</li>
1708 <li>If two structures in one Chimera window, mouseover of
1709 either sequence shows on first structure</li>
1710 <li>'Show annotations' options should not make
1711 non-positional annotations visible</li>
1712 <li>Subsequence secondary structure annotation not shown
1713 in right place after 'view flanking regions'</li>
1714 <li>File Save As type unset when current file format is
1716 <li>Save as '.jar' option removed for saving Jalview
1718 <li>Colour by Sequence colouring in Chimera more
1720 <li>Cannot 'add reference annotation' for a sequence in
1721 several views on same alignment</li>
1722 <li>Cannot show linked products for EMBL / ENA records</li>
1723 <li>Jalview's tooltip wraps long texts containing no
1725 </ul> <em>Applet</em>
1727 <li>Jmol to JalviewLite mouseover/link not working</li>
1728 <li>JalviewLite can't import sequences with ID
1729 descriptions containing angle brackets</li>
1730 </ul> <em>General</em>
1732 <li>Cannot export and reimport RNA secondary structure
1733 via jalview annotation file</li>
1734 <li>Random helix colour palette for colour by annotation
1735 with RNA secondary structure</li>
1736 <li>Mouseover to cDNA from STOP residue in protein
1737 translation doesn't work.</li>
1738 <li>hints when using the select by annotation dialog box</li>
1739 <li>Jmol alignment incorrect if PDB file has alternate CA
1741 <li>FontChooser message dialog appears to hang after
1742 choosing 1pt font</li>
1743 <li>Peptide secondary structure incorrectly imported from
1744 annotation file when annotation display text includes 'e' or
1746 <li>Cannot set colour of new feature type whilst creating
1748 <li>cDNA translation alignment should not be sequence
1749 order dependent</li>
1750 <li>'Show unconserved' doesn't work for lower case
1752 <li>Nucleotide ambiguity codes involving R not recognised</li>
1753 </ul> <em>Deployment and Documentation</em>
1755 <li>Applet example pages appear different to the rest of
1756 www.jalview.org</li>
1757 </ul> <em>Application Known issues</em>
1759 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1760 <li>Misleading message appears after trying to delete
1762 <li>Jalview icon not shown in dock after InstallAnywhere
1763 version launches</li>
1764 <li>Fetching EMBL reference for an RNA sequence results
1765 fails with a sequence mismatch</li>
1766 <li>Corrupted or unreadable alignment display when
1767 scrolling alignment to right</li>
1768 <li>ArrayIndexOutOfBoundsException thrown when remove
1769 empty columns called on alignment with ragged gapped ends</li>
1770 <li>auto calculated alignment annotation rows do not get
1771 placed above or below non-autocalculated rows</li>
1772 <li>Jalview dekstop becomes sluggish at full screen in
1773 ultra-high resolution</li>
1774 <li>Cannot disable consensus calculation independently of
1775 quality and conservation</li>
1776 <li>Mouseover highlighting between cDNA and protein can
1777 become sluggish with more than one splitframe shown</li>
1778 </ul> <em>Applet Known Issues</em>
1780 <li>Core PDB parsing code requires Jmol</li>
1781 <li>Sequence canvas panel goes white when alignment
1782 window is being resized</li>
1788 <td><div align="center">
1789 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1791 <td><em>General</em>
1793 <li>Updated Java code signing certificate donated by
1795 <li>Features and annotation preserved when performing
1796 pairwise alignment</li>
1797 <li>RNA pseudoknot annotation can be
1798 imported/exported/displayed</li>
1799 <li>'colour by annotation' can colour by RNA and
1800 protein secondary structure</li>
1801 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1802 post-hoc with 2.9 release</em>)
1805 </ul> <em>Application</em>
1807 <li>Extract and display secondary structure for sequences
1808 with 3D structures</li>
1809 <li>Support for parsing RNAML</li>
1810 <li>Annotations menu for layout
1812 <li>sort sequence annotation rows by alignment</li>
1813 <li>place sequence annotation above/below alignment
1816 <li>Output in Stockholm format</li>
1817 <li>Internationalisation: improved Spanish (es)
1819 <li>Structure viewer preferences tab</li>
1820 <li>Disorder and Secondary Structure annotation tracks
1821 shared between alignments</li>
1822 <li>UCSF Chimera launch and linked highlighting from
1824 <li>Show/hide all sequence associated annotation rows for
1825 all or current selection</li>
1826 <li>disorder and secondary structure predictions
1827 available as dataset annotation</li>
1828 <li>Per-sequence rna helices colouring</li>
1831 <li>Sequence database accessions imported when fetching
1832 alignments from Rfam</li>
1833 <li>update VARNA version to 3.91</li>
1835 <li>New groovy scripts for exporting aligned positions,
1836 conservation values, and calculating sum of pairs scores.</li>
1837 <li>Command line argument to set default JABAWS server</li>
1838 <li>include installation type in build properties and
1839 console log output</li>
1840 <li>Updated Jalview project format to preserve dataset
1844 <!-- issues resolved --> <em>Application</em>
1846 <li>Distinguish alignment and sequence associated RNA
1847 structure in structure->view->VARNA</li>
1848 <li>Raise dialog box if user deletes all sequences in an
1850 <li>Pressing F1 results in documentation opening twice</li>
1851 <li>Sequence feature tooltip is wrapped</li>
1852 <li>Double click on sequence associated annotation
1853 selects only first column</li>
1854 <li>Redundancy removal doesn't result in unlinked
1855 leaves shown in tree</li>
1856 <li>Undos after several redundancy removals don't undo
1858 <li>Hide sequence doesn't hide associated annotation</li>
1859 <li>User defined colours dialog box too big to fit on
1860 screen and buttons not visible</li>
1861 <li>author list isn't updated if already written to
1862 Jalview properties</li>
1863 <li>Popup menu won't open after retrieving sequence
1865 <li>File open window for associate PDB doesn't open</li>
1866 <li>Left-then-right click on a sequence id opens a
1867 browser search window</li>
1868 <li>Cannot open sequence feature shading/sort popup menu
1869 in feature settings dialog</li>
1870 <li>better tooltip placement for some areas of Jalview
1872 <li>Allow addition of JABAWS Server which doesn't
1873 pass validation</li>
1874 <li>Web services parameters dialog box is too large to
1876 <li>Muscle nucleotide alignment preset obscured by
1878 <li>JABAWS preset submenus don't contain newly
1879 defined user preset</li>
1880 <li>MSA web services warns user if they were launched
1881 with invalid input</li>
1882 <li>Jalview cannot contact DAS Registy when running on
1885 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1886 'Superpose with' submenu not shown when new view
1890 </ul> <!-- <em>Applet</em>
1892 </ul> <em>General</em>
1894 </ul>--> <em>Deployment and Documentation</em>
1896 <li>2G and 1G options in launchApp have no effect on
1897 memory allocation</li>
1898 <li>launchApp service doesn't automatically open
1899 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1901 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1902 InstallAnywhere reports cannot find valid JVM when Java
1903 1.7_055 is available
1905 </ul> <em>Application Known issues</em>
1908 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1909 corrupted or unreadable alignment display when scrolling
1913 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1914 retrieval fails but progress bar continues for DAS retrieval
1915 with large number of ID
1918 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1919 flatfile output of visible region has incorrect sequence
1923 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1924 rna structure consensus doesn't update when secondary
1925 structure tracks are rearranged
1928 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1929 invalid rna structure positional highlighting does not
1930 highlight position of invalid base pairs
1933 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1934 out of memory errors are not raised when saving Jalview
1935 project from alignment window file menu
1938 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1939 Switching to RNA Helices colouring doesn't propagate to
1943 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1944 colour by RNA Helices not enabled when user created
1945 annotation added to alignment
1948 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1949 Jalview icon not shown on dock in Mountain Lion/Webstart
1951 </ul> <em>Applet Known Issues</em>
1954 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1955 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1958 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1959 Jalview and Jmol example not compatible with IE9
1962 <li>Sort by annotation score doesn't reverse order
1968 <td><div align="center">
1969 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1972 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1975 <li>Internationalisation of user interface (usually
1976 called i18n support) and translation for Spanish locale</li>
1977 <li>Define/Undefine group on current selection with
1978 Ctrl-G/Shift Ctrl-G</li>
1979 <li>Improved group creation/removal options in
1980 alignment/sequence Popup menu</li>
1981 <li>Sensible precision for symbol distribution
1982 percentages shown in logo tooltip.</li>
1983 <li>Annotation panel height set according to amount of
1984 annotation when alignment first opened</li>
1985 </ul> <em>Application</em>
1987 <li>Interactive consensus RNA secondary structure
1988 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1989 <li>Select columns containing particular features from
1990 Feature Settings dialog</li>
1991 <li>View all 'representative' PDB structures for selected
1993 <li>Update Jalview project format:
1995 <li>New file extension for Jalview projects '.jvp'</li>
1996 <li>Preserve sequence and annotation dataset (to
1997 store secondary structure annotation,etc)</li>
1998 <li>Per group and alignment annotation and RNA helix
2002 <li>New similarity measures for PCA and Tree calculation
2004 <li>Experimental support for retrieval and viewing of
2005 flanking regions for an alignment</li>
2009 <!-- issues resolved --> <em>Application</em>
2011 <li>logo keeps spinning and status remains at queued or
2012 running after job is cancelled</li>
2013 <li>cannot export features from alignments imported from
2014 Jalview/VAMSAS projects</li>
2015 <li>Buggy slider for web service parameters that take
2017 <li>Newly created RNA secondary structure line doesn't
2018 have 'display all symbols' flag set</li>
2019 <li>T-COFFEE alignment score shading scheme and other
2020 annotation shading not saved in Jalview project</li>
2021 <li>Local file cannot be loaded in freshly downloaded
2023 <li>Jalview icon not shown on dock in Mountain
2025 <li>Load file from desktop file browser fails</li>
2026 <li>Occasional NPE thrown when calculating large trees</li>
2027 <li>Cannot reorder or slide sequences after dragging an
2028 alignment onto desktop</li>
2029 <li>Colour by annotation dialog throws NPE after using
2030 'extract scores' function</li>
2031 <li>Loading/cut'n'pasting an empty file leads to a grey
2032 alignment window</li>
2033 <li>Disorder thresholds rendered incorrectly after
2034 performing IUPred disorder prediction</li>
2035 <li>Multiple group annotated consensus rows shown when
2036 changing 'normalise logo' display setting</li>
2037 <li>Find shows blank dialog after 'finished searching' if
2038 nothing matches query</li>
2039 <li>Null Pointer Exceptions raised when sorting by
2040 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2042 <li>Errors in Jmol console when structures in alignment
2043 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2045 <li>Not all working JABAWS services are shown in
2047 <li>JAVAWS version of Jalview fails to launch with
2048 'invalid literal/length code'</li>
2049 <li>Annotation/RNA Helix colourschemes cannot be applied
2050 to alignment with groups (actually fixed in 2.8.0b1)</li>
2051 <li>RNA Helices and T-Coffee Scores available as default
2054 </ul> <em>Applet</em>
2056 <li>Remove group option is shown even when selection is
2058 <li>Apply to all groups ticked but colourscheme changes
2059 don't affect groups</li>
2060 <li>Documented RNA Helices and T-Coffee Scores as valid
2061 colourscheme name</li>
2062 <li>Annotation labels drawn on sequence IDs when
2063 Annotation panel is not displayed</li>
2064 <li>Increased font size for dropdown menus on OSX and
2065 embedded windows</li>
2066 </ul> <em>Other</em>
2068 <li>Consensus sequence for alignments/groups with a
2069 single sequence were not calculated</li>
2070 <li>annotation files that contain only groups imported as
2071 annotation and junk sequences</li>
2072 <li>Fasta files with sequences containing '*' incorrectly
2073 recognised as PFAM or BLC</li>
2074 <li>conservation/PID slider apply all groups option
2075 doesn't affect background (2.8.0b1)
2077 <li>redundancy highlighting is erratic at 0% and 100%</li>
2078 <li>Remove gapped columns fails for sequences with ragged
2080 <li>AMSA annotation row with leading spaces is not
2081 registered correctly on import</li>
2082 <li>Jalview crashes when selecting PCA analysis for
2083 certain alignments</li>
2084 <li>Opening the colour by annotation dialog for an
2085 existing annotation based 'use original colours'
2086 colourscheme loses original colours setting</li>
2091 <td><div align="center">
2092 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2093 <em>30/1/2014</em></strong>
2097 <li>Trusted certificates for JalviewLite applet and
2098 Jalview Desktop application<br />Certificate was donated by
2099 <a href="https://www.certum.eu">Certum</a> to the Jalview
2100 open source project).
2102 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2103 <li>Output in Stockholm format</li>
2104 <li>Allow import of data from gzipped files</li>
2105 <li>Export/import group and sequence associated line
2106 graph thresholds</li>
2107 <li>Nucleotide substitution matrix that supports RNA and
2108 ambiguity codes</li>
2109 <li>Allow disorder predictions to be made on the current
2110 selection (or visible selection) in the same way that JPred
2112 <li>Groovy scripting for headless Jalview operation</li>
2113 </ul> <em>Other improvements</em>
2115 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2116 <li>COMBINE statement uses current SEQUENCE_REF and
2117 GROUP_REF scope to group annotation rows</li>
2118 <li>Support '' style escaping of quotes in Newick
2120 <li>Group options for JABAWS service by command line name</li>
2121 <li>Empty tooltip shown for JABA service options with a
2122 link but no description</li>
2123 <li>Select primary source when selecting authority in
2124 database fetcher GUI</li>
2125 <li>Add .mfa to FASTA file extensions recognised by
2127 <li>Annotation label tooltip text wrap</li>
2132 <li>Slow scrolling when lots of annotation rows are
2134 <li>Lots of NPE (and slowness) after creating RNA
2135 secondary structure annotation line</li>
2136 <li>Sequence database accessions not imported when
2137 fetching alignments from Rfam</li>
2138 <li>Incorrect SHMR submission for sequences with
2140 <li>View all structures does not always superpose
2142 <li>Option widgets in service parameters not updated to
2143 reflect user or preset settings</li>
2144 <li>Null pointer exceptions for some services without
2145 presets or adjustable parameters</li>
2146 <li>Discover PDB IDs entry in structure menu doesn't
2147 discover PDB xRefs</li>
2148 <li>Exception encountered while trying to retrieve
2149 features with DAS</li>
2150 <li>Lowest value in annotation row isn't coloured
2151 when colour by annotation (per sequence) is coloured</li>
2152 <li>Keyboard mode P jumps to start of gapped region when
2153 residue follows a gap</li>
2154 <li>Jalview appears to hang importing an alignment with
2155 Wrap as default or after enabling Wrap</li>
2156 <li>'Right click to add annotations' message
2157 shown in wrap mode when no annotations present</li>
2158 <li>Disorder predictions fail with NPE if no automatic
2159 annotation already exists on alignment</li>
2160 <li>oninit javascript function should be called after
2161 initialisation completes</li>
2162 <li>Remove redundancy after disorder prediction corrupts
2163 alignment window display</li>
2164 <li>Example annotation file in documentation is invalid</li>
2165 <li>Grouped line graph annotation rows are not exported
2166 to annotation file</li>
2167 <li>Multi-harmony analysis cannot be run when only two
2169 <li>Cannot create multiple groups of line graphs with
2170 several 'combine' statements in annotation file</li>
2171 <li>Pressing return several times causes Number Format
2172 exceptions in keyboard mode</li>
2173 <li>Multi-harmony (SHMMR) method doesn't submit
2174 correct partitions for input data</li>
2175 <li>Translation from DNA to Amino Acids fails</li>
2176 <li>Jalview fail to load newick tree with quoted label</li>
2177 <li>--headless flag isn't understood</li>
2178 <li>ClassCastException when generating EPS in headless
2180 <li>Adjusting sequence-associated shading threshold only
2181 changes one row's threshold</li>
2182 <li>Preferences and Feature settings panel panel
2183 doesn't open</li>
2184 <li>hide consensus histogram also hides conservation and
2185 quality histograms</li>
2190 <td><div align="center">
2191 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2193 <td><em>Application</em>
2195 <li>Support for JABAWS 2.0 Services (AACon alignment
2196 conservation, protein disorder and Clustal Omega)</li>
2197 <li>JABAWS server status indicator in Web Services
2199 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2200 in Jalview alignment window</li>
2201 <li>Updated Jalview build and deploy framework for OSX
2202 mountain lion, windows 7, and 8</li>
2203 <li>Nucleotide substitution matrix for PCA that supports
2204 RNA and ambiguity codes</li>
2206 <li>Improved sequence database retrieval GUI</li>
2207 <li>Support fetching and database reference look up
2208 against multiple DAS sources (Fetch all from in 'fetch db
2210 <li>Jalview project improvements
2212 <li>Store and retrieve the 'belowAlignment'
2213 flag for annotation</li>
2214 <li>calcId attribute to group annotation rows on the
2216 <li>Store AACon calculation settings for a view in
2217 Jalview project</li>
2221 <li>horizontal scrolling gesture support</li>
2222 <li>Visual progress indicator when PCA calculation is
2224 <li>Simpler JABA web services menus</li>
2225 <li>visual indication that web service results are still
2226 being retrieved from server</li>
2227 <li>Serialise the dialogs that are shown when Jalview
2228 starts up for first time</li>
2229 <li>Jalview user agent string for interacting with HTTP
2231 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2233 <li>Examples directory and Groovy library included in
2234 InstallAnywhere distribution</li>
2235 </ul> <em>Applet</em>
2237 <li>RNA alignment and secondary structure annotation
2238 visualization applet example</li>
2239 </ul> <em>General</em>
2241 <li>Normalise option for consensus sequence logo</li>
2242 <li>Reset button in PCA window to return dimensions to
2244 <li>Allow seqspace or Jalview variant of alignment PCA
2246 <li>PCA with either nucleic acid and protein substitution
2248 <li>Allow windows containing HTML reports to be exported
2250 <li>Interactive display and editing of RNA secondary
2251 structure contacts</li>
2252 <li>RNA Helix Alignment Colouring</li>
2253 <li>RNA base pair logo consensus</li>
2254 <li>Parse sequence associated secondary structure
2255 information in Stockholm files</li>
2256 <li>HTML Export database accessions and annotation
2257 information presented in tooltip for sequences</li>
2258 <li>Import secondary structure from LOCARNA clustalw
2259 style RNA alignment files</li>
2260 <li>import and visualise T-COFFEE quality scores for an
2262 <li>'colour by annotation' per sequence option to
2263 shade each sequence according to its associated alignment
2265 <li>New Jalview Logo</li>
2266 </ul> <em>Documentation and Development</em>
2268 <li>documentation for score matrices used in Jalview</li>
2269 <li>New Website!</li>
2271 <td><em>Application</em>
2273 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2274 wsdbfetch REST service</li>
2275 <li>Stop windows being moved outside desktop on OSX</li>
2276 <li>Filetype associations not installed for webstart
2278 <li>Jalview does not always retrieve progress of a JABAWS
2279 job execution in full once it is complete</li>
2280 <li>revise SHMR RSBS definition to ensure alignment is
2281 uploaded via ali_file parameter</li>
2282 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2283 <li>View all structures superposed fails with exception</li>
2284 <li>Jnet job queues forever if a very short sequence is
2285 submitted for prediction</li>
2286 <li>Cut and paste menu not opened when mouse clicked on
2288 <li>Putting fractional value into integer text box in
2289 alignment parameter dialog causes Jalview to hang</li>
2290 <li>Structure view highlighting doesn't work on
2292 <li>View all structures fails with exception shown in
2294 <li>Characters in filename associated with PDBEntry not
2295 escaped in a platform independent way</li>
2296 <li>Jalview desktop fails to launch with exception when
2298 <li>Tree calculation reports 'you must have 2 or more
2299 sequences selected' when selection is empty</li>
2300 <li>Jalview desktop fails to launch with jar signature
2301 failure when java web start temporary file caching is
2303 <li>DAS Sequence retrieval with range qualification
2304 results in sequence xref which includes range qualification</li>
2305 <li>Errors during processing of command line arguments
2306 cause progress bar (JAL-898) to be removed</li>
2307 <li>Replace comma for semi-colon option not disabled for
2308 DAS sources in sequence fetcher</li>
2309 <li>Cannot close news reader when JABAWS server warning
2310 dialog is shown</li>
2311 <li>Option widgets not updated to reflect user settings</li>
2312 <li>Edited sequence not submitted to web service</li>
2313 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2314 <li>InstallAnywhere installer doesn't unpack and run
2315 on OSX Mountain Lion</li>
2316 <li>Annotation panel not given a scroll bar when
2317 sequences with alignment annotation are pasted into the
2319 <li>Sequence associated annotation rows not associated
2320 when loaded from Jalview project</li>
2321 <li>Browser launch fails with NPE on java 1.7</li>
2322 <li>JABAWS alignment marked as finished when job was
2323 cancelled or job failed due to invalid input</li>
2324 <li>NPE with v2.7 example when clicking on Tree
2325 associated with all views</li>
2326 <li>Exceptions when copy/paste sequences with grouped
2327 annotation rows to new window</li>
2328 </ul> <em>Applet</em>
2330 <li>Sequence features are momentarily displayed before
2331 they are hidden using hidefeaturegroups applet parameter</li>
2332 <li>loading features via javascript API automatically
2333 enables feature display</li>
2334 <li>scrollToColumnIn javascript API method doesn't
2336 </ul> <em>General</em>
2338 <li>Redundancy removal fails for rna alignment</li>
2339 <li>PCA calculation fails when sequence has been selected
2340 and then deselected</li>
2341 <li>PCA window shows grey box when first opened on OSX</li>
2342 <li>Letters coloured pink in sequence logo when alignment
2343 coloured with clustalx</li>
2344 <li>Choosing fonts without letter symbols defined causes
2345 exceptions and redraw errors</li>
2346 <li>Initial PCA plot view is not same as manually
2347 reconfigured view</li>
2348 <li>Grouped annotation graph label has incorrect line
2350 <li>Grouped annotation graph label display is corrupted
2351 for lots of labels</li>
2356 <div align="center">
2357 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2360 <td><em>Application</em>
2362 <li>Jalview Desktop News Reader</li>
2363 <li>Tweaked default layout of web services menu</li>
2364 <li>View/alignment association menu to enable user to
2365 easily specify which alignment a multi-structure view takes
2366 its colours/correspondences from</li>
2367 <li>Allow properties file location to be specified as URL</li>
2368 <li>Extend Jalview project to preserve associations
2369 between many alignment views and a single Jmol display</li>
2370 <li>Store annotation row height in Jalview project file</li>
2371 <li>Annotation row column label formatting attributes
2372 stored in project file</li>
2373 <li>Annotation row order for auto-calculated annotation
2374 rows preserved in Jalview project file</li>
2375 <li>Visual progress indication when Jalview state is
2376 saved using Desktop window menu</li>
2377 <li>Visual indication that command line arguments are
2378 still being processed</li>
2379 <li>Groovy script execution from URL</li>
2380 <li>Colour by annotation default min and max colours in
2382 <li>Automatically associate PDB files dragged onto an
2383 alignment with sequences that have high similarity and
2385 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2386 <li>'view structures' option to open many
2387 structures in same window</li>
2388 <li>Sort associated views menu option for tree panel</li>
2389 <li>Group all JABA and non-JABA services for a particular
2390 analysis function in its own submenu</li>
2391 </ul> <em>Applet</em>
2393 <li>Userdefined and autogenerated annotation rows for
2395 <li>Adjustment of alignment annotation pane height</li>
2396 <li>Annotation scrollbar for annotation panel</li>
2397 <li>Drag to reorder annotation rows in annotation panel</li>
2398 <li>'automaticScrolling' parameter</li>
2399 <li>Allow sequences with partial ID string matches to be
2400 annotated from GFF/Jalview features files</li>
2401 <li>Sequence logo annotation row in applet</li>
2402 <li>Absolute paths relative to host server in applet
2403 parameters are treated as such</li>
2404 <li>New in the JalviewLite javascript API:
2406 <li>JalviewLite.js javascript library</li>
2407 <li>Javascript callbacks for
2409 <li>Applet initialisation</li>
2410 <li>Sequence/alignment mouse-overs and selections</li>
2413 <li>scrollTo row and column alignment scrolling
2415 <li>Select sequence/alignment regions from javascript</li>
2416 <li>javascript structure viewer harness to pass
2417 messages between Jmol and Jalview when running as
2418 distinct applets</li>
2419 <li>sortBy method</li>
2420 <li>Set of applet and application examples shipped
2421 with documentation</li>
2422 <li>New example to demonstrate JalviewLite and Jmol
2423 javascript message exchange</li>
2425 </ul> <em>General</em>
2427 <li>Enable Jmol displays to be associated with multiple
2428 multiple alignments</li>
2429 <li>Option to automatically sort alignment with new tree</li>
2430 <li>User configurable link to enable redirects to a
2431 www.Jalview.org mirror</li>
2432 <li>Jmol colours option for Jmol displays</li>
2433 <li>Configurable newline string when writing alignment
2434 and other flat files</li>
2435 <li>Allow alignment annotation description lines to
2436 contain html tags</li>
2437 </ul> <em>Documentation and Development</em>
2439 <li>Add groovy test harness for bulk load testing to
2441 <li>Groovy script to load and align a set of sequences
2442 using a web service before displaying the result in the
2443 Jalview desktop</li>
2444 <li>Restructured javascript and applet api documentation</li>
2445 <li>Ant target to publish example html files with applet
2447 <li>Netbeans project for building Jalview from source</li>
2448 <li>ant task to create online javadoc for Jalview source</li>
2450 <td><em>Application</em>
2452 <li>User defined colourscheme throws exception when
2453 current built in colourscheme is saved as new scheme</li>
2454 <li>AlignFrame->Save in application pops up save
2455 dialog for valid filename/format</li>
2456 <li>Cannot view associated structure for UniProt sequence</li>
2457 <li>PDB file association breaks for UniProt sequence
2459 <li>Associate PDB from file dialog does not tell you
2460 which sequence is to be associated with the file</li>
2461 <li>Find All raises null pointer exception when query
2462 only matches sequence IDs</li>
2463 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2464 <li>Jalview project with Jmol views created with Jalview
2465 2.4 cannot be loaded</li>
2466 <li>Filetype associations not installed for webstart
2468 <li>Two or more chains in a single PDB file associated
2469 with sequences in different alignments do not get coloured
2470 by their associated sequence</li>
2471 <li>Visibility status of autocalculated annotation row
2472 not preserved when project is loaded</li>
2473 <li>Annotation row height and visibility attributes not
2474 stored in Jalview project</li>
2475 <li>Tree bootstraps are not preserved when saved as a
2476 Jalview project</li>
2477 <li>Envision2 workflow tooltips are corrupted</li>
2478 <li>Enabling show group conservation also enables colour
2479 by conservation</li>
2480 <li>Duplicate group associated conservation or consensus
2481 created on new view</li>
2482 <li>Annotation scrollbar not displayed after 'show
2483 all hidden annotation rows' option selected</li>
2484 <li>Alignment quality not updated after alignment
2485 annotation row is hidden then shown</li>
2486 <li>Preserve colouring of structures coloured by
2487 sequences in pre Jalview 2.7 projects</li>
2488 <li>Web service job parameter dialog is not laid out
2490 <li>Web services menu not refreshed after 'reset
2491 services' button is pressed in preferences</li>
2492 <li>Annotation off by one in Jalview v2_3 example project</li>
2493 <li>Structures imported from file and saved in project
2494 get name like jalview_pdb1234.txt when reloaded</li>
2495 <li>Jalview does not always retrieve progress of a JABAWS
2496 job execution in full once it is complete</li>
2497 </ul> <em>Applet</em>
2499 <li>Alignment height set incorrectly when lots of
2500 annotation rows are displayed</li>
2501 <li>Relative URLs in feature HTML text not resolved to
2503 <li>View follows highlighting does not work for positions
2505 <li><= shown as = in tooltip</li>
2506 <li>Export features raises exception when no features
2508 <li>Separator string used for serialising lists of IDs
2509 for javascript api is modified when separator string
2510 provided as parameter</li>
2511 <li>Null pointer exception when selecting tree leaves for
2512 alignment with no existing selection</li>
2513 <li>Relative URLs for datasources assumed to be relative
2514 to applet's codebase</li>
2515 <li>Status bar not updated after finished searching and
2516 search wraps around to first result</li>
2517 <li>StructureSelectionManager instance shared between
2518 several Jalview applets causes race conditions and memory
2520 <li>Hover tooltip and mouseover of position on structure
2521 not sent from Jmol in applet</li>
2522 <li>Certain sequences of javascript method calls to
2523 applet API fatally hang browser</li>
2524 </ul> <em>General</em>
2526 <li>View follows structure mouseover scrolls beyond
2527 position with wrapped view and hidden regions</li>
2528 <li>Find sequence position moves to wrong residue
2529 with/without hidden columns</li>
2530 <li>Sequence length given in alignment properties window
2532 <li>InvalidNumberFormat exceptions thrown when trying to
2533 import PDB like structure files</li>
2534 <li>Positional search results are only highlighted
2535 between user-supplied sequence start/end bounds</li>
2536 <li>End attribute of sequence is not validated</li>
2537 <li>Find dialog only finds first sequence containing a
2538 given sequence position</li>
2539 <li>Sequence numbering not preserved in MSF alignment
2541 <li>Jalview PDB file reader does not extract sequence
2542 from nucleotide chains correctly</li>
2543 <li>Structure colours not updated when tree partition
2544 changed in alignment</li>
2545 <li>Sequence associated secondary structure not correctly
2546 parsed in interleaved stockholm</li>
2547 <li>Colour by annotation dialog does not restore current
2549 <li>Hiding (nearly) all sequences doesn't work
2551 <li>Sequences containing lowercase letters are not
2552 properly associated with their pdb files</li>
2553 </ul> <em>Documentation and Development</em>
2555 <li>schemas/JalviewWsParamSet.xsd corrupted by
2556 ApplyCopyright tool</li>
2561 <div align="center">
2562 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2565 <td><em>Application</em>
2567 <li>New warning dialog when the Jalview Desktop cannot
2568 contact web services</li>
2569 <li>JABA service parameters for a preset are shown in
2570 service job window</li>
2571 <li>JABA Service menu entries reworded</li>
2575 <li>Modeller PIR IO broken - cannot correctly import a
2576 pir file emitted by Jalview</li>
2577 <li>Existing feature settings transferred to new
2578 alignment view created from cut'n'paste</li>
2579 <li>Improved test for mixed amino/nucleotide chains when
2580 parsing PDB files</li>
2581 <li>Consensus and conservation annotation rows
2582 occasionally become blank for all new windows</li>
2583 <li>Exception raised when right clicking above sequences
2584 in wrapped view mode</li>
2585 </ul> <em>Application</em>
2587 <li>multiple multiply aligned structure views cause cpu
2588 usage to hit 100% and computer to hang</li>
2589 <li>Web Service parameter layout breaks for long user
2590 parameter names</li>
2591 <li>Jaba service discovery hangs desktop if Jaba server
2598 <div align="center">
2599 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2602 <td><em>Application</em>
2604 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2605 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2608 <li>Web Services preference tab</li>
2609 <li>Analysis parameters dialog box and user defined
2611 <li>Improved speed and layout of Envision2 service menu</li>
2612 <li>Superpose structures using associated sequence
2614 <li>Export coordinates and projection as CSV from PCA
2616 </ul> <em>Applet</em>
2618 <li>enable javascript: execution by the applet via the
2619 link out mechanism</li>
2620 </ul> <em>Other</em>
2622 <li>Updated the Jmol Jalview interface to work with Jmol
2624 <li>The Jalview Desktop and JalviewLite applet now
2625 require Java 1.5</li>
2626 <li>Allow Jalview feature colour specification for GFF
2627 sequence annotation files</li>
2628 <li>New 'colour by label' keword in Jalview feature file
2629 type colour specification</li>
2630 <li>New Jalview Desktop Groovy API method that allows a
2631 script to check if it being run in an interactive session or
2632 in a batch operation from the Jalview command line</li>
2636 <li>clustalx colourscheme colours Ds preferentially when
2637 both D+E are present in over 50% of the column</li>
2638 </ul> <em>Application</em>
2640 <li>typo in AlignmentFrame->View->Hide->all but
2641 selected Regions menu item</li>
2642 <li>sequence fetcher replaces ',' for ';' when the ',' is
2643 part of a valid accession ID</li>
2644 <li>fatal OOM if object retrieved by sequence fetcher
2645 runs out of memory</li>
2646 <li>unhandled Out of Memory Error when viewing pca
2647 analysis results</li>
2648 <li>InstallAnywhere builds fail to launch on OS X java
2649 10.5 update 4 (due to apple Java 1.6 update)</li>
2650 <li>Installanywhere Jalview silently fails to launch</li>
2651 </ul> <em>Applet</em>
2653 <li>Jalview.getFeatureGroups() raises an
2654 ArrayIndexOutOfBoundsException if no feature groups are
2661 <div align="center">
2662 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2668 <li>Alignment prettyprinter doesn't cope with long
2670 <li>clustalx colourscheme colours Ds preferentially when
2671 both D+E are present in over 50% of the column</li>
2672 <li>nucleic acid structures retrieved from PDB do not
2673 import correctly</li>
2674 <li>More columns get selected than were clicked on when a
2675 number of columns are hidden</li>
2676 <li>annotation label popup menu not providing correct
2677 add/hide/show options when rows are hidden or none are
2679 <li>Stockholm format shown in list of readable formats,
2680 and parser copes better with alignments from RFAM.</li>
2681 <li>CSV output of consensus only includes the percentage
2682 of all symbols if sequence logo display is enabled</li>
2684 </ul> <em>Applet</em>
2686 <li>annotation panel disappears when annotation is
2688 </ul> <em>Application</em>
2690 <li>Alignment view not redrawn properly when new
2691 alignment opened where annotation panel is visible but no
2692 annotations are present on alignment</li>
2693 <li>pasted region containing hidden columns is
2694 incorrectly displayed in new alignment window</li>
2695 <li>Jalview slow to complete operations when stdout is
2696 flooded (fix is to close the Jalview console)</li>
2697 <li>typo in AlignmentFrame->View->Hide->all but
2698 selected Rregions menu item.</li>
2699 <li>inconsistent group submenu and Format submenu entry
2700 'Un' or 'Non'conserved</li>
2701 <li>Sequence feature settings are being shared by
2702 multiple distinct alignments</li>
2703 <li>group annotation not recreated when tree partition is
2705 <li>double click on group annotation to select sequences
2706 does not propagate to associated trees</li>
2707 <li>Mac OSX specific issues:
2709 <li>exception raised when mouse clicked on desktop
2710 window background</li>
2711 <li>Desktop menu placed on menu bar and application
2712 name set correctly</li>
2713 <li>sequence feature settings not wide enough for the
2714 save feature colourscheme button</li>
2723 <div align="center">
2724 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2727 <td><em>New Capabilities</em>
2729 <li>URL links generated from description line for
2730 regular-expression based URL links (applet and application)
2732 <li>Non-positional feature URL links are shown in link
2734 <li>Linked viewing of nucleic acid sequences and
2736 <li>Automatic Scrolling option in View menu to display
2737 the currently highlighted region of an alignment.</li>
2738 <li>Order an alignment by sequence length, or using the
2739 average score or total feature count for each sequence.</li>
2740 <li>Shading features by score or associated description</li>
2741 <li>Subdivide alignment and groups based on identity of
2742 selected subsequence (Make Groups from Selection).</li>
2743 <li>New hide/show options including Shift+Control+H to
2744 hide everything but the currently selected region.</li>
2745 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2746 </ul> <em>Application</em>
2748 <li>Fetch DB References capabilities and UI expanded to
2749 support retrieval from DAS sequence sources</li>
2750 <li>Local DAS Sequence sources can be added via the
2751 command line or via the Add local source dialog box.</li>
2752 <li>DAS Dbref and DbxRef feature types are parsed as
2753 database references and protein_name is parsed as
2754 description line (BioSapiens terms).</li>
2755 <li>Enable or disable non-positional feature and database
2756 references in sequence ID tooltip from View menu in
2758 <!-- <li>New hidden columns and rows and representatives capabilities
2759 in annotations file (in progress - not yet fully implemented)</li> -->
2760 <li>Group-associated consensus, sequence logos and
2761 conservation plots</li>
2762 <li>Symbol distributions for each column can be exported
2763 and visualized as sequence logos</li>
2764 <li>Optionally scale multi-character column labels to fit
2765 within each column of annotation row<!-- todo for applet -->
2767 <li>Optional automatic sort of associated alignment view
2768 when a new tree is opened.</li>
2769 <li>Jalview Java Console</li>
2770 <li>Better placement of desktop window when moving
2771 between different screens.</li>
2772 <li>New preference items for sequence ID tooltip and
2773 consensus annotation</li>
2774 <li>Client to submit sequences and IDs to Envision2
2776 <li><em>Vamsas Capabilities</em>
2778 <li>Improved VAMSAS synchronization (Jalview archive
2779 used to preserve views, structures, and tree display
2781 <li>Import of vamsas documents from disk or URL via
2783 <li>Sharing of selected regions between views and
2784 with other VAMSAS applications (Experimental feature!)</li>
2785 <li>Updated API to VAMSAS version 0.2</li>
2787 </ul> <em>Applet</em>
2789 <li>Middle button resizes annotation row height</li>
2792 <li>sortByTree (true/false) - automatically sort the
2793 associated alignment view by the tree when a new tree is
2795 <li>showTreeBootstraps (true/false) - show or hide
2796 branch bootstraps (default is to show them if available)</li>
2797 <li>showTreeDistances (true/false) - show or hide
2798 branch lengths (default is to show them if available)</li>
2799 <li>showUnlinkedTreeNodes (true/false) - indicate if
2800 unassociated nodes should be highlighted in the tree
2802 <li>heightScale and widthScale (1.0 or more) -
2803 increase the height or width of a cell in the alignment
2804 grid relative to the current font size.</li>
2807 <li>Non-positional features displayed in sequence ID
2809 </ul> <em>Other</em>
2811 <li>Features format: graduated colour definitions and
2812 specification of feature scores</li>
2813 <li>Alignment Annotations format: new keywords for group
2814 associated annotation (GROUP_REF) and annotation row display
2815 properties (ROW_PROPERTIES)</li>
2816 <li>XML formats extended to support graduated feature
2817 colourschemes, group associated annotation, and profile
2818 visualization settings.</li></td>
2821 <li>Source field in GFF files parsed as feature source
2822 rather than description</li>
2823 <li>Non-positional features are now included in sequence
2824 feature and gff files (controlled via non-positional feature
2825 visibility in tooltip).</li>
2826 <li>URL links generated for all feature links (bugfix)</li>
2827 <li>Added URL embedding instructions to features file
2829 <li>Codons containing ambiguous nucleotides translated as
2830 'X' in peptide product</li>
2831 <li>Match case switch in find dialog box works for both
2832 sequence ID and sequence string and query strings do not
2833 have to be in upper case to match case-insensitively.</li>
2834 <li>AMSA files only contain first column of
2835 multi-character column annotation labels</li>
2836 <li>Jalview Annotation File generation/parsing consistent
2837 with documentation (e.g. Stockholm annotation can be
2838 exported and re-imported)</li>
2839 <li>PDB files without embedded PDB IDs given a friendly
2841 <li>Find incrementally searches ID string matches as well
2842 as subsequence matches, and correctly reports total number
2846 <li>Better handling of exceptions during sequence
2848 <li>Dasobert generated non-positional feature URL
2849 link text excludes the start_end suffix</li>
2850 <li>DAS feature and source retrieval buttons disabled
2851 when fetch or registry operations in progress.</li>
2852 <li>PDB files retrieved from URLs are cached properly</li>
2853 <li>Sequence description lines properly shared via
2855 <li>Sequence fetcher fetches multiple records for all
2857 <li>Ensured that command line das feature retrieval
2858 completes before alignment figures are generated.</li>
2859 <li>Reduced time taken when opening file browser for
2861 <li>isAligned check prior to calculating tree, PCA or
2862 submitting an MSA to JNet now excludes hidden sequences.</li>
2863 <li>User defined group colours properly recovered
2864 from Jalview projects.</li>
2873 <div align="center">
2874 <strong>2.4.0.b2</strong><br> 28/10/2009
2879 <li>Experimental support for google analytics usage
2881 <li>Jalview privacy settings (user preferences and docs).</li>
2886 <li>Race condition in applet preventing startup in
2888 <li>Exception when feature created from selection beyond
2889 length of sequence.</li>
2890 <li>Allow synthetic PDB files to be imported gracefully</li>
2891 <li>Sequence associated annotation rows associate with
2892 all sequences with a given id</li>
2893 <li>Find function matches case-insensitively for sequence
2894 ID string searches</li>
2895 <li>Non-standard characters do not cause pairwise
2896 alignment to fail with exception</li>
2897 </ul> <em>Application Issues</em>
2899 <li>Sequences are now validated against EMBL database</li>
2900 <li>Sequence fetcher fetches multiple records for all
2902 </ul> <em>InstallAnywhere Issues</em>
2904 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2905 issue with installAnywhere mechanism)</li>
2906 <li>Command line launching of JARs from InstallAnywhere
2907 version (java class versioning error fixed)</li>
2914 <div align="center">
2915 <strong>2.4</strong><br> 27/8/2008
2918 <td><em>User Interface</em>
2920 <li>Linked highlighting of codon and amino acid from
2921 translation and protein products</li>
2922 <li>Linked highlighting of structure associated with
2923 residue mapping to codon position</li>
2924 <li>Sequence Fetcher provides example accession numbers
2925 and 'clear' button</li>
2926 <li>MemoryMonitor added as an option under Desktop's
2928 <li>Extract score function to parse whitespace separated
2929 numeric data in description line</li>
2930 <li>Column labels in alignment annotation can be centred.</li>
2931 <li>Tooltip for sequence associated annotation give name
2933 </ul> <em>Web Services and URL fetching</em>
2935 <li>JPred3 web service</li>
2936 <li>Prototype sequence search client (no public services
2938 <li>Fetch either seed alignment or full alignment from
2940 <li>URL Links created for matching database cross
2941 references as well as sequence ID</li>
2942 <li>URL Links can be created using regular-expressions</li>
2943 </ul> <em>Sequence Database Connectivity</em>
2945 <li>Retrieval of cross-referenced sequences from other
2947 <li>Generalised database reference retrieval and
2948 validation to all fetchable databases</li>
2949 <li>Fetch sequences from DAS sources supporting the
2950 sequence command</li>
2951 </ul> <em>Import and Export</em>
2952 <li>export annotation rows as CSV for spreadsheet import</li>
2953 <li>Jalview projects record alignment dataset associations,
2954 EMBL products, and cDNA sequence mappings</li>
2955 <li>Sequence Group colour can be specified in Annotation
2957 <li>Ad-hoc colouring of group in Annotation File using RGB
2958 triplet as name of colourscheme</li>
2959 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2961 <li>treenode binding for VAMSAS tree exchange</li>
2962 <li>local editing and update of sequences in VAMSAS
2963 alignments (experimental)</li>
2964 <li>Create new or select existing session to join</li>
2965 <li>load and save of vamsas documents</li>
2966 </ul> <em>Application command line</em>
2968 <li>-tree parameter to open trees (introduced for passing
2970 <li>-fetchfrom command line argument to specify nicknames
2971 of DAS servers to query for alignment features</li>
2972 <li>-dasserver command line argument to add new servers
2973 that are also automatically queried for features</li>
2974 <li>-groovy command line argument executes a given groovy
2975 script after all input data has been loaded and parsed</li>
2976 </ul> <em>Applet-Application data exchange</em>
2978 <li>Trees passed as applet parameters can be passed to
2979 application (when using "View in full
2980 application")</li>
2981 </ul> <em>Applet Parameters</em>
2983 <li>feature group display control parameter</li>
2984 <li>debug parameter</li>
2985 <li>showbutton parameter</li>
2986 </ul> <em>Applet API methods</em>
2988 <li>newView public method</li>
2989 <li>Window (current view) specific get/set public methods</li>
2990 <li>Feature display control methods</li>
2991 <li>get list of currently selected sequences</li>
2992 </ul> <em>New Jalview distribution features</em>
2994 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2995 <li>RELEASE file gives build properties for the latest
2996 Jalview release.</li>
2997 <li>Java 1.1 Applet build made easier and donotobfuscate
2998 property controls execution of obfuscator</li>
2999 <li>Build target for generating source distribution</li>
3000 <li>Debug flag for javacc</li>
3001 <li>.jalview_properties file is documented (slightly) in
3002 jalview.bin.Cache</li>
3003 <li>Continuous Build Integration for stable and
3004 development version of Application, Applet and source
3009 <li>selected region output includes visible annotations
3010 (for certain formats)</li>
3011 <li>edit label/displaychar contains existing label/char
3013 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3014 <li>shorter peptide product names from EMBL records</li>
3015 <li>Newick string generator makes compact representations</li>
3016 <li>bootstrap values parsed correctly for tree files with
3018 <li>pathological filechooser bug avoided by not allowing
3019 filenames containing a ':'</li>
3020 <li>Fixed exception when parsing GFF files containing
3021 global sequence features</li>
3022 <li>Alignment datasets are finalized only when number of
3023 references from alignment sequences goes to zero</li>
3024 <li>Close of tree branch colour box without colour
3025 selection causes cascading exceptions</li>
3026 <li>occasional negative imgwidth exceptions</li>
3027 <li>better reporting of non-fatal warnings to user when
3028 file parsing fails.</li>
3029 <li>Save works when Jalview project is default format</li>
3030 <li>Save as dialog opened if current alignment format is
3031 not a valid output format</li>
3032 <li>UniProt canonical names introduced for both das and
3034 <li>Histidine should be midblue (not pink!) in Zappo</li>
3035 <li>error messages passed up and output when data read
3037 <li>edit undo recovers previous dataset sequence when
3038 sequence is edited</li>
3039 <li>allow PDB files without pdb ID HEADER lines (like
3040 those generated by MODELLER) to be read in properly</li>
3041 <li>allow reading of JPred concise files as a normal
3043 <li>Stockholm annotation parsing and alignment properties
3044 import fixed for PFAM records</li>
3045 <li>Structure view windows have correct name in Desktop
3047 <li>annotation consisting of sequence associated scores
3048 can be read and written correctly to annotation file</li>
3049 <li>Aligned cDNA translation to aligned peptide works
3051 <li>Fixed display of hidden sequence markers and
3052 non-italic font for representatives in Applet</li>
3053 <li>Applet Menus are always embedded in applet window on
3055 <li>Newly shown features appear at top of stack (in
3057 <li>Annotations added via parameter not drawn properly
3058 due to null pointer exceptions</li>
3059 <li>Secondary structure lines are drawn starting from
3060 first column of alignment</li>
3061 <li>UniProt XML import updated for new schema release in
3063 <li>Sequence feature to sequence ID match for Features
3064 file is case-insensitive</li>
3065 <li>Sequence features read from Features file appended to
3066 all sequences with matching IDs</li>
3067 <li>PDB structure coloured correctly for associated views
3068 containing a sub-sequence</li>
3069 <li>PDB files can be retrieved by applet from Jar files</li>
3070 <li>feature and annotation file applet parameters
3071 referring to different directories are retrieved correctly</li>
3072 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3073 <li>Fixed application hang whilst waiting for
3074 splash-screen version check to complete</li>
3075 <li>Applet properly URLencodes input parameter values
3076 when passing them to the launchApp service</li>
3077 <li>display name and local features preserved in results
3078 retrieved from web service</li>
3079 <li>Visual delay indication for sequence retrieval and
3080 sequence fetcher initialisation</li>
3081 <li>updated Application to use DAS 1.53e version of
3082 dasobert DAS client</li>
3083 <li>Re-instated Full AMSA support and .amsa file
3085 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3093 <div align="center">
3094 <strong>2.3</strong><br> 9/5/07
3099 <li>Jmol 11.0.2 integration</li>
3100 <li>PDB views stored in Jalview XML files</li>
3101 <li>Slide sequences</li>
3102 <li>Edit sequence in place</li>
3103 <li>EMBL CDS features</li>
3104 <li>DAS Feature mapping</li>
3105 <li>Feature ordering</li>
3106 <li>Alignment Properties</li>
3107 <li>Annotation Scores</li>
3108 <li>Sort by scores</li>
3109 <li>Feature/annotation editing in applet</li>
3114 <li>Headless state operation in 2.2.1</li>
3115 <li>Incorrect and unstable DNA pairwise alignment</li>
3116 <li>Cut and paste of sequences with annotation</li>
3117 <li>Feature group display state in XML</li>
3118 <li>Feature ordering in XML</li>
3119 <li>blc file iteration selection using filename # suffix</li>
3120 <li>Stockholm alignment properties</li>
3121 <li>Stockhom alignment secondary structure annotation</li>
3122 <li>2.2.1 applet had no feature transparency</li>
3123 <li>Number pad keys can be used in cursor mode</li>
3124 <li>Structure Viewer mirror image resolved</li>
3131 <div align="center">
3132 <strong>2.2.1</strong><br> 12/2/07
3137 <li>Non standard characters can be read and displayed
3138 <li>Annotations/Features can be imported/exported to the
3140 <li>Applet allows editing of sequence/annotation/group
3141 name & description
3142 <li>Preference setting to display sequence name in
3144 <li>Annotation file format extended to allow
3145 Sequence_groups to be defined
3146 <li>Default opening of alignment overview panel can be
3147 specified in preferences
3148 <li>PDB residue numbering annotation added to associated
3154 <li>Applet crash under certain Linux OS with Java 1.6
3156 <li>Annotation file export / import bugs fixed
3157 <li>PNG / EPS image output bugs fixed
3163 <div align="center">
3164 <strong>2.2</strong><br> 27/11/06
3169 <li>Multiple views on alignment
3170 <li>Sequence feature editing
3171 <li>"Reload" alignment
3172 <li>"Save" to current filename
3173 <li>Background dependent text colour
3174 <li>Right align sequence ids
3175 <li>User-defined lower case residue colours
3178 <li>Menu item accelerator keys
3179 <li>Control-V pastes to current alignment
3180 <li>Cancel button for DAS Feature Fetching
3181 <li>PCA and PDB Viewers zoom via mouse roller
3182 <li>User-defined sub-tree colours and sub-tree selection
3184 <li>'New Window' button on the 'Output to Text box'
3189 <li>New memory efficient Undo/Redo System
3190 <li>Optimised symbol lookups and conservation/consensus
3192 <li>Region Conservation/Consensus recalculated after
3194 <li>Fixed Remove Empty Columns Bug (empty columns at end
3196 <li>Slowed DAS Feature Fetching for increased robustness.
3198 <li>Made angle brackets in ASCII feature descriptions
3200 <li>Re-instated Zoom function for PCA
3201 <li>Sequence descriptions conserved in web service
3203 <li>UniProt ID discoverer uses any word separated by
3205 <li>WsDbFetch query/result association resolved
3206 <li>Tree leaf to sequence mapping improved
3207 <li>Smooth fonts switch moved to FontChooser dialog box.
3214 <div align="center">
3215 <strong>2.1.1</strong><br> 12/9/06
3220 <li>Copy consensus sequence to clipboard</li>
3225 <li>Image output - rightmost residues are rendered if
3226 sequence id panel has been resized</li>
3227 <li>Image output - all offscreen group boundaries are
3229 <li>Annotation files with sequence references - all
3230 elements in file are relative to sequence position</li>
3231 <li>Mac Applet users can use Alt key for group editing</li>
3237 <div align="center">
3238 <strong>2.1</strong><br> 22/8/06
3243 <li>MAFFT Multiple Alignment in default Web Service list</li>
3244 <li>DAS Feature fetching</li>
3245 <li>Hide sequences and columns</li>
3246 <li>Export Annotations and Features</li>
3247 <li>GFF file reading / writing</li>
3248 <li>Associate structures with sequences from local PDB
3250 <li>Add sequences to exisiting alignment</li>
3251 <li>Recently opened files / URL lists</li>
3252 <li>Applet can launch the full application</li>
3253 <li>Applet has transparency for features (Java 1.2
3255 <li>Applet has user defined colours parameter</li>
3256 <li>Applet can load sequences from parameter
3257 "sequence<em>x</em>"
3263 <li>Redundancy Panel reinstalled in the Applet</li>
3264 <li>Monospaced font - EPS / rescaling bug fixed</li>
3265 <li>Annotation files with sequence references bug fixed</li>
3271 <div align="center">
3272 <strong>2.08.1</strong><br> 2/5/06
3277 <li>Change case of selected region from Popup menu</li>
3278 <li>Choose to match case when searching</li>
3279 <li>Middle mouse button and mouse movement can compress /
3280 expand the visible width and height of the alignment</li>
3285 <li>Annotation Panel displays complete JNet results</li>
3291 <div align="center">
3292 <strong>2.08b</strong><br> 18/4/06
3298 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3299 <li>Righthand label on wrapped alignments shows correct
3306 <div align="center">
3307 <strong>2.08</strong><br> 10/4/06
3312 <li>Editing can be locked to the selection area</li>
3313 <li>Keyboard editing</li>
3314 <li>Create sequence features from searches</li>
3315 <li>Precalculated annotations can be loaded onto
3317 <li>Features file allows grouping of features</li>
3318 <li>Annotation Colouring scheme added</li>
3319 <li>Smooth fonts off by default - Faster rendering</li>
3320 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3325 <li>Drag & Drop fixed on Linux</li>
3326 <li>Jalview Archive file faster to load/save, sequence
3327 descriptions saved.</li>
3333 <div align="center">
3334 <strong>2.07</strong><br> 12/12/05
3339 <li>PDB Structure Viewer enhanced</li>
3340 <li>Sequence Feature retrieval and display enhanced</li>
3341 <li>Choose to output sequence start-end after sequence
3342 name for file output</li>
3343 <li>Sequence Fetcher WSDBFetch@EBI</li>
3344 <li>Applet can read feature files, PDB files and can be
3345 used for HTML form input</li>
3350 <li>HTML output writes groups and features</li>
3351 <li>Group editing is Control and mouse click</li>
3352 <li>File IO bugs</li>
3358 <div align="center">
3359 <strong>2.06</strong><br> 28/9/05
3364 <li>View annotations in wrapped mode</li>
3365 <li>More options for PCA viewer</li>
3370 <li>GUI bugs resolved</li>
3371 <li>Runs with -nodisplay from command line</li>
3377 <div align="center">
3378 <strong>2.05b</strong><br> 15/9/05
3383 <li>Choose EPS export as lineart or text</li>
3384 <li>Jar files are executable</li>
3385 <li>Can read in Uracil - maps to unknown residue</li>
3390 <li>Known OutOfMemory errors give warning message</li>
3391 <li>Overview window calculated more efficiently</li>
3392 <li>Several GUI bugs resolved</li>
3398 <div align="center">
3399 <strong>2.05</strong><br> 30/8/05
3404 <li>Edit and annotate in "Wrapped" view</li>
3409 <li>Several GUI bugs resolved</li>
3415 <div align="center">
3416 <strong>2.04</strong><br> 24/8/05
3421 <li>Hold down mouse wheel & scroll to change font
3427 <li>Improved JPred client reliability</li>
3428 <li>Improved loading of Jalview files</li>
3434 <div align="center">
3435 <strong>2.03</strong><br> 18/8/05
3440 <li>Set Proxy server name and port in preferences</li>
3441 <li>Multiple URL links from sequence ids</li>
3442 <li>User Defined Colours can have a scheme name and added
3444 <li>Choose to ignore gaps in consensus calculation</li>
3445 <li>Unix users can set default web browser</li>
3446 <li>Runs without GUI for batch processing</li>
3447 <li>Dynamically generated Web Service Menus</li>
3452 <li>InstallAnywhere download for Sparc Solaris</li>
3458 <div align="center">
3459 <strong>2.02</strong><br> 18/7/05
3465 <li>Copy & Paste order of sequences maintains
3466 alignment order.</li>
3472 <div align="center">
3473 <strong>2.01</strong><br> 12/7/05
3478 <li>Use delete key for deleting selection.</li>
3479 <li>Use Mouse wheel to scroll sequences.</li>
3480 <li>Help file updated to describe how to add alignment
3482 <li>Version and build date written to build properties
3484 <li>InstallAnywhere installation will check for updates
3485 at launch of Jalview.</li>
3490 <li>Delete gaps bug fixed.</li>
3491 <li>FileChooser sorts columns.</li>
3492 <li>Can remove groups one by one.</li>
3493 <li>Filechooser icons installed.</li>
3494 <li>Finder ignores return character when searching.
3495 Return key will initiate a search.<br>
3502 <div align="center">
3503 <strong>2.0</strong><br> 20/6/05
3508 <li>New codebase</li>