3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <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.2.10.2b1">2.10.2b1</a><br />
77 <td><div align="left">
82 <td><div align="left">
86 <!-- JAL-2681 -->duplicate protein sequences shown after
87 retreiving Ensembl crossrefs for sequences from Uniprot
93 <td width="60" nowrap>
95 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
98 <td><div align="left">
103 <!-- JAL-1933 -->Occupancy annotation row shows number of
104 ungapped positions in each column of the alignment.
107 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
108 a calculation dialog box
111 <!-- JAL-2379 -->Revised implementation of PCA for speed
112 and memory efficiency (~30x faster)
115 <!-- JAL-2403 -->Revised implementation of sequence
116 similarity scores as used by Tree, PCA, Shading Consensus
117 and other calculations
120 <!-- JAL-2416 -->Score matrices are stored as resource
121 files within the Jalview codebase
124 <!-- JAL-2500 -->Trees computed on Sequence Feature
125 Similarity may have different topology due to increased
132 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
133 model for alignments and groups
136 <!-- JAL-384 -->Custom shading schemes created via groovy
143 <!-- JAL-2526 -->Efficiency improvements for interacting
144 with alignment and overview windows
147 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
151 <!-- JAL-2388 -->Hidden columns and sequences can be
155 <!-- JAL-2611 -->Click-drag in visible area allows fine
156 adjustment of visible position
160 <em>Data import/export</em>
163 <!-- JAL-2535 -->Posterior probability annotation from
164 Stockholm files imported as sequence associated annotation
167 <!-- JAL-2507 -->More robust per-sequence positional
168 annotation input/output via stockholm flatfile
171 <!-- JAL-2533 -->Sequence names don't include file
172 extension when importing structure files without embedded
173 names or PDB accessions
176 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
177 format sequence substitution matrices
180 <em>User Interface</em>
183 <!-- JAL-2447 --> Experimental Features Checkbox in
184 Desktop's Tools menu to hide or show untested features in
188 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
189 via Overview or sequence motif search operations
192 <!-- JAL-2547 -->Amend sequence features dialog box can be
193 opened by double clicking gaps within sequence feature
197 <!-- JAL-1476 -->Status bar message shown when not enough
198 aligned positions were available to create a 3D structure
202 <em>3D Structure</em>
205 <!-- JAL-2430 -->Hidden regions in alignment views are not
206 coloured in linked structure views
209 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
210 file-based command exchange
213 <!-- JAL-2375 -->Structure chooser automatically shows
214 Cached Structures rather than querying the PDBe if
215 structures are already available for sequences
218 <!-- JAL-2520 -->Structures imported via URL are cached in
219 the Jalview project rather than downloaded again when the
223 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
224 to transfer Chimera's structure attributes as Jalview
225 features, and vice-versa (<strong>Experimental
229 <em>Web Services</em>
232 <!-- JAL-2549 -->Updated JABAWS client to v2.2
235 <!-- JAL-2335 -->Filter non-standard amino acids and
236 nucleotides when submitting to AACon and other MSA
240 <!-- JAL-2316, -->URLs for viewing database
241 cross-references provided by identifiers.org and the
249 <!-- JAL-2344 -->FileFormatI interface for describing and
250 identifying file formats (instead of String constants)
253 <!-- JAL-2228 -->FeatureCounter script refactored for
254 efficiency when counting all displayed features (not
255 backwards compatible with 2.10.1)
258 <em>Example files</em>
261 <!-- JAL-2631 -->Graduated feature colour style example
262 included in the example feature file
265 <em>Documentation</em>
268 <!-- JAL-2339 -->Release notes reformatted for readability
269 with the built-in Java help viewer
272 <!-- JAL-1644 -->Find documentation updated with 'search
273 sequence description' option
279 <!-- JAL-2485, -->External service integration tests for
280 Uniprot REST Free Text Search Client
283 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
286 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
291 <td><div align="left">
292 <em>Calculations</em>
295 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
296 matrix - C->R should be '-3'<br />Old matrix restored
297 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
299 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
300 Jalview's treatment of gaps in PCA and substitution matrix
301 based Tree calculations.<br /> <br />In earlier versions
302 of Jalview, gaps matching gaps were penalised, and gaps
303 matching non-gaps penalised even more. In the PCA
304 calculation, gaps were actually treated as non-gaps - so
305 different costs were applied, which meant Jalview's PCAs
306 were different to those produced by SeqSpace.<br />Jalview
307 now treats gaps in the same way as SeqSpace (ie it scores
308 them as 0). <br /> <br />Enter the following in the
309 Groovy console to restore pre-2.10.2 behaviour:<br />
310 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
311 // for 2.10.1 mode <br />
312 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
313 // to restore 2.10.2 mode <br /> <br /> <em>Note:
314 these settings will affect all subsequent tree and PCA
315 calculations (not recommended)</em></li>
317 <!-- JAL-2424 -->Fixed off-by-one bug that affected
318 scaling of branch lengths for trees computed using
319 Sequence Feature Similarity.
322 <!-- JAL-2377 -->PCA calculation could hang when
323 generating output report when working with highly
327 <!-- JAL-2544 --> Sort by features includes features to
328 right of selected region when gaps present on right-hand
332 <em>User Interface</em>
335 <!-- JAL-2346 -->Reopening Colour by annotation dialog
336 doesn't reselect a specific sequence's associated
337 annotation after it was used for colouring a view
340 <!-- JAL-2419 -->Current selection lost if popup menu
341 opened on a region of alignment without groups
344 <!-- JAL-2374 -->Popup menu not always shown for regions
345 of an alignment with overlapping groups
348 <!-- JAL-2310 -->Finder double counts if both a sequence's
349 name and description match
352 <!-- JAL-2370 -->Hiding column selection containing two
353 hidden regions results in incorrect hidden regions
356 <!-- JAL-2386 -->'Apply to all groups' setting when
357 changing colour does not apply Conservation slider value
361 <!-- JAL-2373 -->Percentage identity and conservation menu
362 items do not show a tick or allow shading to be disabled
365 <!-- JAL-2385 -->Conservation shading or PID threshold
366 lost when base colourscheme changed if slider not visible
369 <!-- JAL-2547 -->Sequence features shown in tooltip for
370 gaps before start of features
373 <!-- JAL-2623 -->Graduated feature colour threshold not
374 restored to UI when feature colour is edited
377 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
378 a time when scrolling vertically in wrapped mode.
381 <!-- JAL-2630 -->Structure and alignment overview update
382 as graduate feature colour settings are modified via the
386 <!-- JAL-2034 -->Overview window doesn't always update
387 when a group defined on the alignment is resized
390 <!-- JAL-2605 -->Mouseovers on left/right scale region in
391 wrapped view result in positional status updates
395 <!-- JAL-2563 -->Status bar doesn't show position for
396 ambiguous amino acid and nucleotide symbols
399 <!-- JAL-2602 -->Copy consensus sequence failed if
400 alignment included gapped columns
403 <!-- JAL-2473 -->Minimum size set for Jalview windows so
404 widgets don't permanently disappear
407 <!-- JAL-2503 -->Cannot select or filter quantitative
408 annotation that are shown only as column labels (e.g.
409 T-Coffee column reliability scores)
412 <!-- JAL-2594 -->Exception thrown if trying to create a
413 sequence feature on gaps only
416 <!-- JAL-2504 -->Features created with 'New feature'
417 button from a Find inherit previously defined feature type
418 rather than the Find query string
421 <!-- JAL-2423 -->incorrect title in output window when
422 exporting tree calculated in Jalview
425 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
426 and then revealing them reorders sequences on the
430 <!-- JAL-964 -->Group panel in sequence feature settings
431 doesn't update to reflect available set of groups after
432 interactively adding or modifying features
435 <!-- JAL-2225 -->Sequence Database chooser unusable on
439 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
440 only excluded gaps in current sequence and ignored
447 <!-- JAL-2421 -->Overview window visible region moves
448 erratically when hidden rows or columns are present
451 <!-- JAL-2362 -->Per-residue colourschemes applied via the
452 Structure Viewer's colour menu don't correspond to
456 <!-- JAL-2405 -->Protein specific colours only offered in
457 colour and group colour menu for protein alignments
460 <!-- JAL-2385 -->Colour threshold slider doesn't update to
461 reflect currently selected view or group's shading
465 <!-- JAL-2624 -->Feature colour thresholds not respected
466 when rendered on overview and structures when opacity at
470 <!-- JAL-2589 -->User defined gap colour not shown in
471 overview when features overlaid on alignment
474 <em>Data import/export</em>
477 <!-- JAL-2576 -->Very large alignments take a long time to
481 <!-- JAL-2507 -->Per-sequence RNA secondary structures
482 added after a sequence was imported are not written to
486 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
487 when importing RNA secondary structure via Stockholm
490 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
491 not shown in correct direction for simple pseudoknots
494 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
495 with lightGray or darkGray via features file (but can
499 <!-- JAL-2383 -->Above PID colour threshold not recovered
500 when alignment view imported from project
503 <!-- JAL-2520,JAL-2465 -->No mappings generated between
504 structure and sequences extracted from structure files
505 imported via URL and viewed in Jmol
508 <!-- JAL-2520 -->Structures loaded via URL are saved in
509 Jalview Projects rather than fetched via URL again when
510 the project is loaded and the structure viewed
513 <em>Web Services</em>
516 <!-- JAL-2519 -->EnsemblGenomes example failing after
517 release of Ensembl v.88
520 <!-- JAL-2366 -->Proxy server address and port always
521 appear enabled in Preferences->Connections
524 <!-- JAL-2461 -->DAS registry not found exceptions
525 removed from console output
528 <!-- JAL-2582 -->Cannot retrieve protein products from
529 Ensembl by Peptide ID
532 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
533 created from SIFTs, and spurious 'Couldn't open structure
534 in Chimera' errors raised after April 2017 update (problem
535 due to 'null' string rather than empty string used for
536 residues with no corresponding PDB mapping).
539 <em>Application UI</em>
542 <!-- JAL-2361 -->User Defined Colours not added to Colour
546 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
547 case' residues (button in colourscheme editor debugged and
548 new documentation and tooltips added)
551 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
552 doesn't restore group-specific text colour thresholds
555 <!-- JAL-2243 -->Feature settings panel does not update as
556 new features are added to alignment
559 <!-- JAL-2532 -->Cancel in feature settings reverts
560 changes to feature colours via the Amend features dialog
563 <!-- JAL-2506 -->Null pointer exception when attempting to
564 edit graduated feature colour via amend features dialog
568 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
569 selection menu changes colours of alignment views
572 <!-- JAL-2426 -->Spurious exceptions in console raised
573 from alignment calculation workers after alignment has
577 <!-- JAL-1608 -->Typo in selection popup menu - Create
578 groups now 'Create Group'
581 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
582 Create/Undefine group doesn't always work
585 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
586 shown again after pressing 'Cancel'
589 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
590 adjusts start position in wrap mode
593 <!-- JAL-2563 -->Status bar doesn't show positions for
594 ambiguous amino acids
597 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
598 CDS/Protein view after CDS sequences added for aligned
602 <!-- JAL-2592 -->User defined colourschemes called 'User
603 Defined' don't appear in Colours menu
609 <!-- JAL-2468 -->Switching between Nucleotide and Protein
610 score models doesn't always result in an updated PCA plot
613 <!-- JAL-2442 -->Features not rendered as transparent on
614 overview or linked structure view
617 <!-- JAL-2372 -->Colour group by conservation doesn't
621 <!-- JAL-2517 -->Hitting Cancel after applying
622 user-defined colourscheme doesn't restore original
629 <!-- JAL-2314 -->Unit test failure:
630 jalview.ws.jabaws.RNAStructExportImport setup fails
633 <!-- JAL-2307 -->Unit test failure:
634 jalview.ws.sifts.SiftsClientTest due to compatibility
635 problems with deep array comparison equality asserts in
636 successive versions of TestNG
639 <!-- JAL-2479 -->Relocated StructureChooserTest and
640 ParameterUtilsTest Unit tests to Network suite
643 <em>New Known Issues</em>
646 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
647 phase after a sequence motif find operation
650 <!-- JAL-2550 -->Importing annotation file with rows
651 containing just upper and lower case letters are
652 interpreted as WUSS RNA secondary structure symbols
655 <!-- JAL-2590 -->Cannot load and display Newick trees
656 reliably from eggnog Ortholog database
659 <!-- JAL-2468 -->Status bar shows 'Marked x columns
660 containing features of type Highlight' when 'B' is pressed
661 to mark columns containing highlighted regions.
664 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
665 doesn't always add secondary structure annotation.
670 <td width="60" nowrap>
672 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
675 <td><div align="left">
679 <!-- JAL-98 -->Improved memory usage: sparse arrays used
680 for all consensus calculations
683 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
686 <li>Updated Jalview's Certum code signing certificate
692 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
693 set of database cross-references, sorted alphabetically
696 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
697 from database cross references. Users with custom links
698 will receive a <a href="webServices/urllinks.html#warning">warning
699 dialog</a> asking them to update their preferences.
702 <!-- JAL-2287-->Cancel button and escape listener on
703 dialog warning user about disconnecting Jalview from a
707 <!-- JAL-2320-->Jalview's Chimera control window closes if
708 the Chimera it is connected to is shut down
711 <!-- JAL-1738-->New keystroke (B) and Select highlighted
712 columns menu item to mark columns containing highlighted
713 regions (e.g. from structure selections or results of a
717 <!-- JAL-2284-->Command line option for batch-generation
718 of HTML pages rendering alignment data with the BioJS
728 <!-- JAL-2286 -->Columns with more than one modal residue
729 are not coloured or thresholded according to percent
730 identity (first observed in Jalview 2.8.2)
733 <!-- JAL-2301 -->Threonine incorrectly reported as not
737 <!-- JAL-2318 -->Updates to documentation pages (above PID
738 threshold, amino acid properties)
741 <!-- JAL-2292 -->Lower case residues in sequences are not
742 reported as mapped to residues in a structure file in the
746 <!--JAL-2324 -->Identical features with non-numeric scores
747 could be added multiple times to a sequence
750 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
751 bond features shown as two highlighted residues rather
752 than a range in linked structure views, and treated
753 correctly when selecting and computing trees from features
756 <!-- JAL-2281-->Custom URL links for database
757 cross-references are matched to database name regardless
765 <!-- JAL-2282-->Custom URL links for specific database
766 names without regular expressions also offer links from
770 <!-- JAL-2315-->Removing a single configured link in the
771 URL links pane in Connections preferences doesn't actually
772 update Jalview configuration
775 <!-- JAL-2272-->CTRL-Click on a selected region to open
776 the alignment area popup menu doesn't work on El-Capitan
779 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
780 files with similarly named sequences if dropped onto the
784 <!-- JAL-2312 -->Additional mappings are shown for PDB
785 entries where more chains exist in the PDB accession than
786 are reported in the SIFTS file
789 <!-- JAL-2317-->Certain structures do not get mapped to
790 the structure view when displayed with Chimera
793 <!-- JAL-2317-->No chains shown in the Chimera view
794 panel's View->Show Chains submenu
797 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
798 work for wrapped alignment views
801 <!--JAL-2197 -->Rename UI components for running JPred
802 predictions from 'JNet' to 'JPred'
805 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
806 corrupted when annotation panel vertical scroll is not at
810 <!--JAL-2332 -->Attempting to view structure for Hen
811 lysozyme results in a PDB Client error dialog box
814 <!-- JAL-2319 -->Structure View's mapping report switched
815 ranges for PDB and sequence for SIFTS
818 SIFTS 'Not_Observed' residues mapped to non-existant
822 <!-- <em>New Known Issues</em>
829 <td width="60" nowrap>
831 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
832 <em>25/10/2016</em></strong>
835 <td><em>Application</em>
837 <li>3D Structure chooser opens with 'Cached structures'
838 view if structures already loaded</li>
839 <li>Progress bar reports models as they are loaded to
846 <li>Colour by conservation always enabled and no tick
847 shown in menu when BLOSUM or PID shading applied</li>
848 <li>FER1_ARATH and FER2_ARATH labels were switched in
849 example sequences/projects/trees</li>
853 <li>Jalview projects with views of local PDB structure
854 files saved on Windows cannot be opened on OSX</li>
855 <li>Multiple structure views can be opened and superposed
856 without timeout for structures with multiple models or
857 multiple sequences in alignment</li>
858 <li>Cannot import or associated local PDB files without a
859 PDB ID HEADER line</li>
860 <li>RMSD is not output in Jmol console when superposition
862 <li>Drag and drop of URL from Browser fails for Linux and
863 OSX versions earlier than El Capitan</li>
864 <li>ENA client ignores invalid content from ENA server</li>
865 <li>Exceptions are not raised in console when ENA client
866 attempts to fetch non-existent IDs via Fetch DB Refs UI
868 <li>Exceptions are not raised in console when a new view
869 is created on the alignment</li>
870 <li>OSX right-click fixed for group selections: CMD-click
871 to insert/remove gaps in groups and CTRL-click to open group
874 <em>Build and deployment</em>
876 <li>URL link checker now copes with multi-line anchor
879 <em>New Known Issues</em>
881 <li>Drag and drop from URL links in browsers do not work
888 <td width="60" nowrap>
890 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
896 <!-- JAL-2124 -->Updated Spanish translations.
899 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
900 for importing structure data to Jalview. Enables mmCIF and
904 <!-- JAL-192 --->Alignment ruler shows positions relative to
908 <!-- JAL-2202 -->Position/residue shown in status bar when
909 mousing over sequence associated annotation
912 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
916 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
917 '()', canonical '[]' and invalid '{}' base pair populations
921 <!-- JAL-2092 -->Feature settings popup menu options for
922 showing or hiding columns containing a feature
925 <!-- JAL-1557 -->Edit selected group by double clicking on
926 group and sequence associated annotation labels
929 <!-- JAL-2236 -->Sequence name added to annotation label in
930 select/hide columns by annotation and colour by annotation
934 </ul> <em>Application</em>
937 <!-- JAL-2050-->Automatically hide introns when opening a
941 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
945 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
946 structure mappings with the EMBL-EBI PDBe SIFTS database
949 <!-- JAL-2079 -->Updated download sites used for Rfam and
950 Pfam sources to xfam.org
953 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
956 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
957 over sequences in Jalview
960 <!-- JAL-2027-->Support for reverse-complement coding
961 regions in ENA and EMBL
964 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
965 for record retrieval via ENA rest API
968 <!-- JAL-2027 -->Support for ENA CDS records with reverse
972 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
973 groovy script execution
976 <!-- JAL-1812 -->New 'execute Groovy script' option in an
977 alignment window's Calculate menu
980 <!-- JAL-1812 -->Allow groovy scripts that call
981 Jalview.getAlignFrames() to run in headless mode
984 <!-- JAL-2068 -->Support for creating new alignment
985 calculation workers from groovy scripts
988 <!-- JAL-1369 --->Store/restore reference sequence in
992 <!-- JAL-1803 -->Chain codes for a sequence's PDB
993 associations are now saved/restored from project
996 <!-- JAL-1993 -->Database selection dialog always shown
997 before sequence fetcher is opened
1000 <!-- JAL-2183 -->Double click on an entry in Jalview's
1001 database chooser opens a sequence fetcher
1004 <!-- JAL-1563 -->Free-text search client for UniProt using
1005 the UniProt REST API
1008 <!-- JAL-2168 -->-nonews command line parameter to prevent
1009 the news reader opening
1012 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1013 querying stored in preferences
1016 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1020 <!-- JAL-1977-->Tooltips shown on database chooser
1023 <!-- JAL-391 -->Reverse complement function in calculate
1024 menu for nucleotide sequences
1027 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1028 and feature counts preserves alignment ordering (and
1029 debugged for complex feature sets).
1032 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1033 viewing structures with Jalview 2.10
1036 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1037 genome, transcript CCDS and gene ids via the Ensembl and
1038 Ensembl Genomes REST API
1041 <!-- JAL-2049 -->Protein sequence variant annotation
1042 computed for 'sequence_variant' annotation on CDS regions
1046 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1050 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1051 Ref Fetcher fails to match, or otherwise updates sequence
1052 data from external database records.
1055 <!-- JAL-2154 -->Revised Jalview Project format for
1056 efficient recovery of sequence coding and alignment
1057 annotation relationships.
1059 </ul> <!-- <em>Applet</em>
1070 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1074 <!-- JAL-2018-->Export features in Jalview format (again)
1075 includes graduated colourschemes
1078 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1079 working with big alignments and lots of hidden columns
1082 <!-- JAL-2053-->Hidden column markers not always rendered
1083 at right of alignment window
1086 <!-- JAL-2067 -->Tidied up links in help file table of
1090 <!-- JAL-2072 -->Feature based tree calculation not shown
1094 <!-- JAL-2075 -->Hidden columns ignored during feature
1095 based tree calculation
1098 <!-- JAL-2065 -->Alignment view stops updating when show
1099 unconserved enabled for group on alignment
1102 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1106 <!-- JAL-2146 -->Alignment column in status incorrectly
1107 shown as "Sequence position" when mousing over
1111 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1112 hidden columns present
1115 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1116 user created annotation added to alignment
1119 <!-- JAL-1841 -->RNA Structure consensus only computed for
1120 '()' base pair annotation
1123 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1124 in zero scores for all base pairs in RNA Structure
1128 <!-- JAL-2174-->Extend selection with columns containing
1132 <!-- JAL-2275 -->Pfam format writer puts extra space at
1133 beginning of sequence
1136 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1140 <!-- JAL-2238 -->Cannot create groups on an alignment from
1141 from a tree when t-coffee scores are shown
1144 <!-- JAL-1836,1967 -->Cannot import and view PDB
1145 structures with chains containing negative resnums (4q4h)
1148 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1152 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1153 to Clustal, PIR and PileUp output
1156 <!-- JAL-2008 -->Reordering sequence features that are
1157 not visible causes alignment window to repaint
1160 <!-- JAL-2006 -->Threshold sliders don't work in
1161 graduated colour and colour by annotation row for e-value
1162 scores associated with features and annotation rows
1165 <!-- JAL-1797 -->amino acid physicochemical conservation
1166 calculation should be case independent
1169 <!-- JAL-2173 -->Remove annotation also updates hidden
1173 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1174 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1175 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1178 <!-- JAL-2065 -->Null pointer exceptions and redraw
1179 problems when reference sequence defined and 'show
1180 non-conserved' enabled
1183 <!-- JAL-1306 -->Quality and Conservation are now shown on
1184 load even when Consensus calculation is disabled
1187 <!-- JAL-1932 -->Remove right on penultimate column of
1188 alignment does nothing
1191 <em>Application</em>
1194 <!-- JAL-1552-->URLs and links can't be imported by
1195 drag'n'drop on OSX when launched via webstart (note - not
1196 yet fixed for El Capitan)
1199 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1200 output when running on non-gb/us i18n platforms
1203 <!-- JAL-1944 -->Error thrown when exporting a view with
1204 hidden sequences as flat-file alignment
1207 <!-- JAL-2030-->InstallAnywhere distribution fails when
1211 <!-- JAL-2080-->Jalview very slow to launch via webstart
1212 (also hotfix for 2.9.0b2)
1215 <!-- JAL-2085 -->Cannot save project when view has a
1216 reference sequence defined
1219 <!-- JAL-1011 -->Columns are suddenly selected in other
1220 alignments and views when revealing hidden columns
1223 <!-- JAL-1989 -->Hide columns not mirrored in complement
1224 view in a cDNA/Protein splitframe
1227 <!-- JAL-1369 -->Cannot save/restore representative
1228 sequence from project when only one sequence is
1232 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1233 in Structure Chooser
1236 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1237 structure consensus didn't refresh annotation panel
1240 <!-- JAL-1962 -->View mapping in structure view shows
1241 mappings between sequence and all chains in a PDB file
1244 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1245 dialogs format columns correctly, don't display array
1246 data, sort columns according to type
1249 <!-- JAL-1975 -->Export complete shown after destination
1250 file chooser is cancelled during an image export
1253 <!-- JAL-2025 -->Error when querying PDB Service with
1254 sequence name containing special characters
1257 <!-- JAL-2024 -->Manual PDB structure querying should be
1261 <!-- JAL-2104 -->Large tooltips with broken HTML
1262 formatting don't wrap
1265 <!-- JAL-1128 -->Figures exported from wrapped view are
1266 truncated so L looks like I in consensus annotation
1269 <!-- JAL-2003 -->Export features should only export the
1270 currently displayed features for the current selection or
1274 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1275 after fetching cross-references, and restoring from
1279 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1280 followed in the structure viewer
1283 <!-- JAL-2163 -->Titles for individual alignments in
1284 splitframe not restored from project
1287 <!-- JAL-2145 -->missing autocalculated annotation at
1288 trailing end of protein alignment in transcript/product
1289 splitview when pad-gaps not enabled by default
1292 <!-- JAL-1797 -->amino acid physicochemical conservation
1296 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1297 article has been read (reopened issue due to
1298 internationalisation problems)
1301 <!-- JAL-1960 -->Only offer PDB structures in structure
1302 viewer based on sequence name, PDB and UniProt
1307 <!-- JAL-1976 -->No progress bar shown during export of
1311 <!-- JAL-2213 -->Structures not always superimposed after
1312 multiple structures are shown for one or more sequences.
1315 <!-- JAL-1370 -->Reference sequence characters should not
1316 be replaced with '.' when 'Show unconserved' format option
1320 <!-- JAL-1823 -->Cannot specify chain code when entering
1321 specific PDB id for sequence
1324 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1325 'Export hidden sequences' is enabled, but 'export hidden
1326 columns' is disabled.
1329 <!--JAL-2026-->Best Quality option in structure chooser
1330 selects lowest rather than highest resolution structures
1334 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1335 to sequence mapping in 'View Mappings' report
1338 <!-- JAL-2284 -->Unable to read old Jalview projects that
1339 contain non-XML data added after Jalvew wrote project.
1342 <!-- JAL-2118 -->Newly created annotation row reorders
1343 after clicking on it to create new annotation for a
1346 <!-- may exclude, this is an external service stability issue JAL-1941
1347 -- > RNA 3D structure not added via DSSR service</li> -->
1352 <!-- JAL-2151 -->Incorrect columns are selected when
1353 hidden columns present before start of sequence
1356 <!-- JAL-1986 -->Missing dependencies on applet pages
1360 <!-- JAL-1947 -->Overview pixel size changes when
1361 sequences are hidden in applet
1364 <!-- JAL-1996 -->Updated instructions for applet
1365 deployment on examples pages.
1372 <td width="60" nowrap>
1373 <div align="center">
1374 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1375 <em>16/10/2015</em></strong>
1378 <td><em>General</em>
1380 <li>Time stamps for signed Jalview application and applet
1385 <em>Application</em>
1387 <li>Duplicate group consensus and conservation rows
1388 shown when tree is partitioned</li>
1389 <li>Erratic behaviour when tree partitions made with
1390 multiple cDNA/Protein split views</li>
1396 <td width="60" nowrap>
1397 <div align="center">
1398 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1399 <em>8/10/2015</em></strong>
1402 <td><em>General</em>
1404 <li>Updated Spanish translations of localized text for
1406 </ul> <em>Application</em>
1408 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1409 <li>Signed OSX InstallAnywhere installer<br></li>
1410 <li>Support for per-sequence based annotations in BioJSON</li>
1411 </ul> <em>Applet</em>
1413 <li>Split frame example added to applet examples page</li>
1414 </ul> <em>Build and Deployment</em>
1417 <!-- JAL-1888 -->New ant target for running Jalview's test
1425 <li>Mapping of cDNA to protein in split frames
1426 incorrect when sequence start > 1</li>
1427 <li>Broken images in filter column by annotation dialog
1429 <li>Feature colours not parsed from features file</li>
1430 <li>Exceptions and incomplete link URLs recovered when
1431 loading a features file containing HTML tags in feature
1435 <em>Application</em>
1437 <li>Annotations corrupted after BioJS export and
1439 <li>Incorrect sequence limits after Fetch DB References
1440 with 'trim retrieved sequences'</li>
1441 <li>Incorrect warning about deleting all data when
1442 deleting selected columns</li>
1443 <li>Patch to build system for shipping properly signed
1444 JNLP templates for webstart launch</li>
1445 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1446 unreleased structures for download or viewing</li>
1447 <li>Tab/space/return keystroke operation of EMBL-PDBe
1448 fetcher/viewer dialogs works correctly</li>
1449 <li>Disabled 'minimise' button on Jalview windows
1450 running on OSX to workaround redraw hang bug</li>
1451 <li>Split cDNA/Protein view position and geometry not
1452 recovered from jalview project</li>
1453 <li>Initial enabled/disabled state of annotation menu
1454 sorter 'show autocalculated first/last' corresponds to
1456 <li>Restoring of Clustal, RNA Helices and T-Coffee
1457 color schemes from BioJSON</li>
1461 <li>Reorder sequences mirrored in cDNA/Protein split
1463 <li>Applet with Jmol examples not loading correctly</li>
1469 <td><div align="center">
1470 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1472 <td><em>General</em>
1474 <li>Linked visualisation and analysis of DNA and Protein
1477 <li>Translated cDNA alignments shown as split protein
1478 and DNA alignment views</li>
1479 <li>Codon consensus annotation for linked protein and
1480 cDNA alignment views</li>
1481 <li>Link cDNA or Protein product sequences by loading
1482 them onto Protein or cDNA alignments</li>
1483 <li>Reconstruct linked cDNA alignment from aligned
1484 protein sequences</li>
1487 <li>Jmol integration updated to Jmol v14.2.14</li>
1488 <li>Import and export of Jalview alignment views as <a
1489 href="features/bioJsonFormat.html">BioJSON</a></li>
1490 <li>New alignment annotation file statements for
1491 reference sequences and marking hidden columns</li>
1492 <li>Reference sequence based alignment shading to
1493 highlight variation</li>
1494 <li>Select or hide columns according to alignment
1496 <li>Find option for locating sequences by description</li>
1497 <li>Conserved physicochemical properties shown in amino
1498 acid conservation row</li>
1499 <li>Alignments can be sorted by number of RNA helices</li>
1500 </ul> <em>Application</em>
1502 <li>New cDNA/Protein analysis capabilities
1504 <li>Get Cross-References should open a Split Frame
1505 view with cDNA/Protein</li>
1506 <li>Detect when nucleotide sequences and protein
1507 sequences are placed in the same alignment</li>
1508 <li>Split cDNA/Protein views are saved in Jalview
1513 <li>Use REST API to talk to Chimera</li>
1514 <li>Selected regions in Chimera are highlighted in linked
1515 Jalview windows</li>
1517 <li>VARNA RNA viewer updated to v3.93</li>
1518 <li>VARNA views are saved in Jalview Projects</li>
1519 <li>Pseudoknots displayed as Jalview RNA annotation can
1520 be shown in VARNA</li>
1522 <li>Make groups for selection uses marked columns as well
1523 as the active selected region</li>
1525 <li>Calculate UPGMA and NJ trees using sequence feature
1527 <li>New Export options
1529 <li>New Export Settings dialog to control hidden
1530 region export in flat file generation</li>
1532 <li>Export alignment views for display with the <a
1533 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1535 <li>Export scrollable SVG in HTML page</li>
1536 <li>Optional embedding of BioJSON data when exporting
1537 alignment figures to HTML</li>
1539 <li>3D structure retrieval and display
1541 <li>Free text and structured queries with the PDBe
1543 <li>PDBe Search API based discovery and selection of
1544 PDB structures for a sequence set</li>
1548 <li>JPred4 employed for protein secondary structure
1550 <li>Hide Insertions menu option to hide unaligned columns
1551 for one or a group of sequences</li>
1552 <li>Automatically hide insertions in alignments imported
1553 from the JPred4 web server</li>
1554 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1555 system on OSX<br />LGPL libraries courtesy of <a
1556 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1558 <li>changed 'View nucleotide structure' submenu to 'View
1559 VARNA 2D Structure'</li>
1560 <li>change "View protein structure" menu option to "3D
1563 </ul> <em>Applet</em>
1565 <li>New layout for applet example pages</li>
1566 <li>New parameters to enable SplitFrame view
1567 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1568 <li>New example demonstrating linked viewing of cDNA and
1569 Protein alignments</li>
1570 </ul> <em>Development and deployment</em>
1572 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1573 <li>Include installation type and git revision in build
1574 properties and console log output</li>
1575 <li>Jalview Github organisation, and new github site for
1576 storing BioJsMSA Templates</li>
1577 <li>Jalview's unit tests now managed with TestNG</li>
1580 <!-- <em>General</em>
1582 </ul> --> <!-- issues resolved --> <em>Application</em>
1584 <li>Escape should close any open find dialogs</li>
1585 <li>Typo in select-by-features status report</li>
1586 <li>Consensus RNA secondary secondary structure
1587 predictions are not highlighted in amber</li>
1588 <li>Missing gap character in v2.7 example file means
1589 alignment appears unaligned when pad-gaps is not enabled</li>
1590 <li>First switch to RNA Helices colouring doesn't colour
1591 associated structure views</li>
1592 <li>ID width preference option is greyed out when auto
1593 width checkbox not enabled</li>
1594 <li>Stopped a warning dialog from being shown when
1595 creating user defined colours</li>
1596 <li>'View Mapping' in structure viewer shows sequence
1597 mappings for just that viewer's sequences</li>
1598 <li>Workaround for superposing PDB files containing
1599 multiple models in Chimera</li>
1600 <li>Report sequence position in status bar when hovering
1601 over Jmol structure</li>
1602 <li>Cannot output gaps as '.' symbols with Selection ->
1603 output to text box</li>
1604 <li>Flat file exports of alignments with hidden columns
1605 have incorrect sequence start/end</li>
1606 <li>'Aligning' a second chain to a Chimera structure from
1608 <li>Colour schemes applied to structure viewers don't
1609 work for nucleotide</li>
1610 <li>Loading/cut'n'pasting an empty or invalid file leads
1611 to a grey/invisible alignment window</li>
1612 <li>Exported Jpred annotation from a sequence region
1613 imports to different position</li>
1614 <li>Space at beginning of sequence feature tooltips shown
1615 on some platforms</li>
1616 <li>Chimera viewer 'View | Show Chain' menu is not
1618 <li>'New View' fails with a Null Pointer Exception in
1619 console if Chimera has been opened</li>
1620 <li>Mouseover to Chimera not working</li>
1621 <li>Miscellaneous ENA XML feature qualifiers not
1623 <li>NPE in annotation renderer after 'Extract Scores'</li>
1624 <li>If two structures in one Chimera window, mouseover of
1625 either sequence shows on first structure</li>
1626 <li>'Show annotations' options should not make
1627 non-positional annotations visible</li>
1628 <li>Subsequence secondary structure annotation not shown
1629 in right place after 'view flanking regions'</li>
1630 <li>File Save As type unset when current file format is
1632 <li>Save as '.jar' option removed for saving Jalview
1634 <li>Colour by Sequence colouring in Chimera more
1636 <li>Cannot 'add reference annotation' for a sequence in
1637 several views on same alignment</li>
1638 <li>Cannot show linked products for EMBL / ENA records</li>
1639 <li>Jalview's tooltip wraps long texts containing no
1641 </ul> <em>Applet</em>
1643 <li>Jmol to JalviewLite mouseover/link not working</li>
1644 <li>JalviewLite can't import sequences with ID
1645 descriptions containing angle brackets</li>
1646 </ul> <em>General</em>
1648 <li>Cannot export and reimport RNA secondary structure
1649 via jalview annotation file</li>
1650 <li>Random helix colour palette for colour by annotation
1651 with RNA secondary structure</li>
1652 <li>Mouseover to cDNA from STOP residue in protein
1653 translation doesn't work.</li>
1654 <li>hints when using the select by annotation dialog box</li>
1655 <li>Jmol alignment incorrect if PDB file has alternate CA
1657 <li>FontChooser message dialog appears to hang after
1658 choosing 1pt font</li>
1659 <li>Peptide secondary structure incorrectly imported from
1660 annotation file when annotation display text includes 'e' or
1662 <li>Cannot set colour of new feature type whilst creating
1664 <li>cDNA translation alignment should not be sequence
1665 order dependent</li>
1666 <li>'Show unconserved' doesn't work for lower case
1668 <li>Nucleotide ambiguity codes involving R not recognised</li>
1669 </ul> <em>Deployment and Documentation</em>
1671 <li>Applet example pages appear different to the rest of
1672 www.jalview.org</li>
1673 </ul> <em>Application Known issues</em>
1675 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1676 <li>Misleading message appears after trying to delete
1678 <li>Jalview icon not shown in dock after InstallAnywhere
1679 version launches</li>
1680 <li>Fetching EMBL reference for an RNA sequence results
1681 fails with a sequence mismatch</li>
1682 <li>Corrupted or unreadable alignment display when
1683 scrolling alignment to right</li>
1684 <li>ArrayIndexOutOfBoundsException thrown when remove
1685 empty columns called on alignment with ragged gapped ends</li>
1686 <li>auto calculated alignment annotation rows do not get
1687 placed above or below non-autocalculated rows</li>
1688 <li>Jalview dekstop becomes sluggish at full screen in
1689 ultra-high resolution</li>
1690 <li>Cannot disable consensus calculation independently of
1691 quality and conservation</li>
1692 <li>Mouseover highlighting between cDNA and protein can
1693 become sluggish with more than one splitframe shown</li>
1694 </ul> <em>Applet Known Issues</em>
1696 <li>Core PDB parsing code requires Jmol</li>
1697 <li>Sequence canvas panel goes white when alignment
1698 window is being resized</li>
1704 <td><div align="center">
1705 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1707 <td><em>General</em>
1709 <li>Updated Java code signing certificate donated by
1711 <li>Features and annotation preserved when performing
1712 pairwise alignment</li>
1713 <li>RNA pseudoknot annotation can be
1714 imported/exported/displayed</li>
1715 <li>'colour by annotation' can colour by RNA and
1716 protein secondary structure</li>
1717 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1718 post-hoc with 2.9 release</em>)
1721 </ul> <em>Application</em>
1723 <li>Extract and display secondary structure for sequences
1724 with 3D structures</li>
1725 <li>Support for parsing RNAML</li>
1726 <li>Annotations menu for layout
1728 <li>sort sequence annotation rows by alignment</li>
1729 <li>place sequence annotation above/below alignment
1732 <li>Output in Stockholm format</li>
1733 <li>Internationalisation: improved Spanish (es)
1735 <li>Structure viewer preferences tab</li>
1736 <li>Disorder and Secondary Structure annotation tracks
1737 shared between alignments</li>
1738 <li>UCSF Chimera launch and linked highlighting from
1740 <li>Show/hide all sequence associated annotation rows for
1741 all or current selection</li>
1742 <li>disorder and secondary structure predictions
1743 available as dataset annotation</li>
1744 <li>Per-sequence rna helices colouring</li>
1747 <li>Sequence database accessions imported when fetching
1748 alignments from Rfam</li>
1749 <li>update VARNA version to 3.91</li>
1751 <li>New groovy scripts for exporting aligned positions,
1752 conservation values, and calculating sum of pairs scores.</li>
1753 <li>Command line argument to set default JABAWS server</li>
1754 <li>include installation type in build properties and
1755 console log output</li>
1756 <li>Updated Jalview project format to preserve dataset
1760 <!-- issues resolved --> <em>Application</em>
1762 <li>Distinguish alignment and sequence associated RNA
1763 structure in structure->view->VARNA</li>
1764 <li>Raise dialog box if user deletes all sequences in an
1766 <li>Pressing F1 results in documentation opening twice</li>
1767 <li>Sequence feature tooltip is wrapped</li>
1768 <li>Double click on sequence associated annotation
1769 selects only first column</li>
1770 <li>Redundancy removal doesn't result in unlinked
1771 leaves shown in tree</li>
1772 <li>Undos after several redundancy removals don't undo
1774 <li>Hide sequence doesn't hide associated annotation</li>
1775 <li>User defined colours dialog box too big to fit on
1776 screen and buttons not visible</li>
1777 <li>author list isn't updated if already written to
1778 Jalview properties</li>
1779 <li>Popup menu won't open after retrieving sequence
1781 <li>File open window for associate PDB doesn't open</li>
1782 <li>Left-then-right click on a sequence id opens a
1783 browser search window</li>
1784 <li>Cannot open sequence feature shading/sort popup menu
1785 in feature settings dialog</li>
1786 <li>better tooltip placement for some areas of Jalview
1788 <li>Allow addition of JABAWS Server which doesn't
1789 pass validation</li>
1790 <li>Web services parameters dialog box is too large to
1792 <li>Muscle nucleotide alignment preset obscured by
1794 <li>JABAWS preset submenus don't contain newly
1795 defined user preset</li>
1796 <li>MSA web services warns user if they were launched
1797 with invalid input</li>
1798 <li>Jalview cannot contact DAS Registy when running on
1801 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1802 'Superpose with' submenu not shown when new view
1806 </ul> <!-- <em>Applet</em>
1808 </ul> <em>General</em>
1810 </ul>--> <em>Deployment and Documentation</em>
1812 <li>2G and 1G options in launchApp have no effect on
1813 memory allocation</li>
1814 <li>launchApp service doesn't automatically open
1815 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1817 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1818 InstallAnywhere reports cannot find valid JVM when Java
1819 1.7_055 is available
1821 </ul> <em>Application Known issues</em>
1824 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1825 corrupted or unreadable alignment display when scrolling
1829 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1830 retrieval fails but progress bar continues for DAS retrieval
1831 with large number of ID
1834 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1835 flatfile output of visible region has incorrect sequence
1839 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1840 rna structure consensus doesn't update when secondary
1841 structure tracks are rearranged
1844 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1845 invalid rna structure positional highlighting does not
1846 highlight position of invalid base pairs
1849 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1850 out of memory errors are not raised when saving Jalview
1851 project from alignment window file menu
1854 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1855 Switching to RNA Helices colouring doesn't propagate to
1859 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1860 colour by RNA Helices not enabled when user created
1861 annotation added to alignment
1864 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1865 Jalview icon not shown on dock in Mountain Lion/Webstart
1867 </ul> <em>Applet Known Issues</em>
1870 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1871 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1874 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1875 Jalview and Jmol example not compatible with IE9
1878 <li>Sort by annotation score doesn't reverse order
1884 <td><div align="center">
1885 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1888 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1891 <li>Internationalisation of user interface (usually
1892 called i18n support) and translation for Spanish locale</li>
1893 <li>Define/Undefine group on current selection with
1894 Ctrl-G/Shift Ctrl-G</li>
1895 <li>Improved group creation/removal options in
1896 alignment/sequence Popup menu</li>
1897 <li>Sensible precision for symbol distribution
1898 percentages shown in logo tooltip.</li>
1899 <li>Annotation panel height set according to amount of
1900 annotation when alignment first opened</li>
1901 </ul> <em>Application</em>
1903 <li>Interactive consensus RNA secondary structure
1904 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1905 <li>Select columns containing particular features from
1906 Feature Settings dialog</li>
1907 <li>View all 'representative' PDB structures for selected
1909 <li>Update Jalview project format:
1911 <li>New file extension for Jalview projects '.jvp'</li>
1912 <li>Preserve sequence and annotation dataset (to
1913 store secondary structure annotation,etc)</li>
1914 <li>Per group and alignment annotation and RNA helix
1918 <li>New similarity measures for PCA and Tree calculation
1920 <li>Experimental support for retrieval and viewing of
1921 flanking regions for an alignment</li>
1925 <!-- issues resolved --> <em>Application</em>
1927 <li>logo keeps spinning and status remains at queued or
1928 running after job is cancelled</li>
1929 <li>cannot export features from alignments imported from
1930 Jalview/VAMSAS projects</li>
1931 <li>Buggy slider for web service parameters that take
1933 <li>Newly created RNA secondary structure line doesn't
1934 have 'display all symbols' flag set</li>
1935 <li>T-COFFEE alignment score shading scheme and other
1936 annotation shading not saved in Jalview project</li>
1937 <li>Local file cannot be loaded in freshly downloaded
1939 <li>Jalview icon not shown on dock in Mountain
1941 <li>Load file from desktop file browser fails</li>
1942 <li>Occasional NPE thrown when calculating large trees</li>
1943 <li>Cannot reorder or slide sequences after dragging an
1944 alignment onto desktop</li>
1945 <li>Colour by annotation dialog throws NPE after using
1946 'extract scores' function</li>
1947 <li>Loading/cut'n'pasting an empty file leads to a grey
1948 alignment window</li>
1949 <li>Disorder thresholds rendered incorrectly after
1950 performing IUPred disorder prediction</li>
1951 <li>Multiple group annotated consensus rows shown when
1952 changing 'normalise logo' display setting</li>
1953 <li>Find shows blank dialog after 'finished searching' if
1954 nothing matches query</li>
1955 <li>Null Pointer Exceptions raised when sorting by
1956 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1958 <li>Errors in Jmol console when structures in alignment
1959 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1961 <li>Not all working JABAWS services are shown in
1963 <li>JAVAWS version of Jalview fails to launch with
1964 'invalid literal/length code'</li>
1965 <li>Annotation/RNA Helix colourschemes cannot be applied
1966 to alignment with groups (actually fixed in 2.8.0b1)</li>
1967 <li>RNA Helices and T-Coffee Scores available as default
1970 </ul> <em>Applet</em>
1972 <li>Remove group option is shown even when selection is
1974 <li>Apply to all groups ticked but colourscheme changes
1975 don't affect groups</li>
1976 <li>Documented RNA Helices and T-Coffee Scores as valid
1977 colourscheme name</li>
1978 <li>Annotation labels drawn on sequence IDs when
1979 Annotation panel is not displayed</li>
1980 <li>Increased font size for dropdown menus on OSX and
1981 embedded windows</li>
1982 </ul> <em>Other</em>
1984 <li>Consensus sequence for alignments/groups with a
1985 single sequence were not calculated</li>
1986 <li>annotation files that contain only groups imported as
1987 annotation and junk sequences</li>
1988 <li>Fasta files with sequences containing '*' incorrectly
1989 recognised as PFAM or BLC</li>
1990 <li>conservation/PID slider apply all groups option
1991 doesn't affect background (2.8.0b1)
1993 <li>redundancy highlighting is erratic at 0% and 100%</li>
1994 <li>Remove gapped columns fails for sequences with ragged
1996 <li>AMSA annotation row with leading spaces is not
1997 registered correctly on import</li>
1998 <li>Jalview crashes when selecting PCA analysis for
1999 certain alignments</li>
2000 <li>Opening the colour by annotation dialog for an
2001 existing annotation based 'use original colours'
2002 colourscheme loses original colours setting</li>
2007 <td><div align="center">
2008 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2009 <em>30/1/2014</em></strong>
2013 <li>Trusted certificates for JalviewLite applet and
2014 Jalview Desktop application<br />Certificate was donated by
2015 <a href="https://www.certum.eu">Certum</a> to the Jalview
2016 open source project).
2018 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2019 <li>Output in Stockholm format</li>
2020 <li>Allow import of data from gzipped files</li>
2021 <li>Export/import group and sequence associated line
2022 graph thresholds</li>
2023 <li>Nucleotide substitution matrix that supports RNA and
2024 ambiguity codes</li>
2025 <li>Allow disorder predictions to be made on the current
2026 selection (or visible selection) in the same way that JPred
2028 <li>Groovy scripting for headless Jalview operation</li>
2029 </ul> <em>Other improvements</em>
2031 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2032 <li>COMBINE statement uses current SEQUENCE_REF and
2033 GROUP_REF scope to group annotation rows</li>
2034 <li>Support '' style escaping of quotes in Newick
2036 <li>Group options for JABAWS service by command line name</li>
2037 <li>Empty tooltip shown for JABA service options with a
2038 link but no description</li>
2039 <li>Select primary source when selecting authority in
2040 database fetcher GUI</li>
2041 <li>Add .mfa to FASTA file extensions recognised by
2043 <li>Annotation label tooltip text wrap</li>
2048 <li>Slow scrolling when lots of annotation rows are
2050 <li>Lots of NPE (and slowness) after creating RNA
2051 secondary structure annotation line</li>
2052 <li>Sequence database accessions not imported when
2053 fetching alignments from Rfam</li>
2054 <li>Incorrect SHMR submission for sequences with
2056 <li>View all structures does not always superpose
2058 <li>Option widgets in service parameters not updated to
2059 reflect user or preset settings</li>
2060 <li>Null pointer exceptions for some services without
2061 presets or adjustable parameters</li>
2062 <li>Discover PDB IDs entry in structure menu doesn't
2063 discover PDB xRefs</li>
2064 <li>Exception encountered while trying to retrieve
2065 features with DAS</li>
2066 <li>Lowest value in annotation row isn't coloured
2067 when colour by annotation (per sequence) is coloured</li>
2068 <li>Keyboard mode P jumps to start of gapped region when
2069 residue follows a gap</li>
2070 <li>Jalview appears to hang importing an alignment with
2071 Wrap as default or after enabling Wrap</li>
2072 <li>'Right click to add annotations' message
2073 shown in wrap mode when no annotations present</li>
2074 <li>Disorder predictions fail with NPE if no automatic
2075 annotation already exists on alignment</li>
2076 <li>oninit javascript function should be called after
2077 initialisation completes</li>
2078 <li>Remove redundancy after disorder prediction corrupts
2079 alignment window display</li>
2080 <li>Example annotation file in documentation is invalid</li>
2081 <li>Grouped line graph annotation rows are not exported
2082 to annotation file</li>
2083 <li>Multi-harmony analysis cannot be run when only two
2085 <li>Cannot create multiple groups of line graphs with
2086 several 'combine' statements in annotation file</li>
2087 <li>Pressing return several times causes Number Format
2088 exceptions in keyboard mode</li>
2089 <li>Multi-harmony (SHMMR) method doesn't submit
2090 correct partitions for input data</li>
2091 <li>Translation from DNA to Amino Acids fails</li>
2092 <li>Jalview fail to load newick tree with quoted label</li>
2093 <li>--headless flag isn't understood</li>
2094 <li>ClassCastException when generating EPS in headless
2096 <li>Adjusting sequence-associated shading threshold only
2097 changes one row's threshold</li>
2098 <li>Preferences and Feature settings panel panel
2099 doesn't open</li>
2100 <li>hide consensus histogram also hides conservation and
2101 quality histograms</li>
2106 <td><div align="center">
2107 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2109 <td><em>Application</em>
2111 <li>Support for JABAWS 2.0 Services (AACon alignment
2112 conservation, protein disorder and Clustal Omega)</li>
2113 <li>JABAWS server status indicator in Web Services
2115 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2116 in Jalview alignment window</li>
2117 <li>Updated Jalview build and deploy framework for OSX
2118 mountain lion, windows 7, and 8</li>
2119 <li>Nucleotide substitution matrix for PCA that supports
2120 RNA and ambiguity codes</li>
2122 <li>Improved sequence database retrieval GUI</li>
2123 <li>Support fetching and database reference look up
2124 against multiple DAS sources (Fetch all from in 'fetch db
2126 <li>Jalview project improvements
2128 <li>Store and retrieve the 'belowAlignment'
2129 flag for annotation</li>
2130 <li>calcId attribute to group annotation rows on the
2132 <li>Store AACon calculation settings for a view in
2133 Jalview project</li>
2137 <li>horizontal scrolling gesture support</li>
2138 <li>Visual progress indicator when PCA calculation is
2140 <li>Simpler JABA web services menus</li>
2141 <li>visual indication that web service results are still
2142 being retrieved from server</li>
2143 <li>Serialise the dialogs that are shown when Jalview
2144 starts up for first time</li>
2145 <li>Jalview user agent string for interacting with HTTP
2147 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2149 <li>Examples directory and Groovy library included in
2150 InstallAnywhere distribution</li>
2151 </ul> <em>Applet</em>
2153 <li>RNA alignment and secondary structure annotation
2154 visualization applet example</li>
2155 </ul> <em>General</em>
2157 <li>Normalise option for consensus sequence logo</li>
2158 <li>Reset button in PCA window to return dimensions to
2160 <li>Allow seqspace or Jalview variant of alignment PCA
2162 <li>PCA with either nucleic acid and protein substitution
2164 <li>Allow windows containing HTML reports to be exported
2166 <li>Interactive display and editing of RNA secondary
2167 structure contacts</li>
2168 <li>RNA Helix Alignment Colouring</li>
2169 <li>RNA base pair logo consensus</li>
2170 <li>Parse sequence associated secondary structure
2171 information in Stockholm files</li>
2172 <li>HTML Export database accessions and annotation
2173 information presented in tooltip for sequences</li>
2174 <li>Import secondary structure from LOCARNA clustalw
2175 style RNA alignment files</li>
2176 <li>import and visualise T-COFFEE quality scores for an
2178 <li>'colour by annotation' per sequence option to
2179 shade each sequence according to its associated alignment
2181 <li>New Jalview Logo</li>
2182 </ul> <em>Documentation and Development</em>
2184 <li>documentation for score matrices used in Jalview</li>
2185 <li>New Website!</li>
2187 <td><em>Application</em>
2189 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2190 wsdbfetch REST service</li>
2191 <li>Stop windows being moved outside desktop on OSX</li>
2192 <li>Filetype associations not installed for webstart
2194 <li>Jalview does not always retrieve progress of a JABAWS
2195 job execution in full once it is complete</li>
2196 <li>revise SHMR RSBS definition to ensure alignment is
2197 uploaded via ali_file parameter</li>
2198 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2199 <li>View all structures superposed fails with exception</li>
2200 <li>Jnet job queues forever if a very short sequence is
2201 submitted for prediction</li>
2202 <li>Cut and paste menu not opened when mouse clicked on
2204 <li>Putting fractional value into integer text box in
2205 alignment parameter dialog causes Jalview to hang</li>
2206 <li>Structure view highlighting doesn't work on
2208 <li>View all structures fails with exception shown in
2210 <li>Characters in filename associated with PDBEntry not
2211 escaped in a platform independent way</li>
2212 <li>Jalview desktop fails to launch with exception when
2214 <li>Tree calculation reports 'you must have 2 or more
2215 sequences selected' when selection is empty</li>
2216 <li>Jalview desktop fails to launch with jar signature
2217 failure when java web start temporary file caching is
2219 <li>DAS Sequence retrieval with range qualification
2220 results in sequence xref which includes range qualification</li>
2221 <li>Errors during processing of command line arguments
2222 cause progress bar (JAL-898) to be removed</li>
2223 <li>Replace comma for semi-colon option not disabled for
2224 DAS sources in sequence fetcher</li>
2225 <li>Cannot close news reader when JABAWS server warning
2226 dialog is shown</li>
2227 <li>Option widgets not updated to reflect user settings</li>
2228 <li>Edited sequence not submitted to web service</li>
2229 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2230 <li>InstallAnywhere installer doesn't unpack and run
2231 on OSX Mountain Lion</li>
2232 <li>Annotation panel not given a scroll bar when
2233 sequences with alignment annotation are pasted into the
2235 <li>Sequence associated annotation rows not associated
2236 when loaded from Jalview project</li>
2237 <li>Browser launch fails with NPE on java 1.7</li>
2238 <li>JABAWS alignment marked as finished when job was
2239 cancelled or job failed due to invalid input</li>
2240 <li>NPE with v2.7 example when clicking on Tree
2241 associated with all views</li>
2242 <li>Exceptions when copy/paste sequences with grouped
2243 annotation rows to new window</li>
2244 </ul> <em>Applet</em>
2246 <li>Sequence features are momentarily displayed before
2247 they are hidden using hidefeaturegroups applet parameter</li>
2248 <li>loading features via javascript API automatically
2249 enables feature display</li>
2250 <li>scrollToColumnIn javascript API method doesn't
2252 </ul> <em>General</em>
2254 <li>Redundancy removal fails for rna alignment</li>
2255 <li>PCA calculation fails when sequence has been selected
2256 and then deselected</li>
2257 <li>PCA window shows grey box when first opened on OSX</li>
2258 <li>Letters coloured pink in sequence logo when alignment
2259 coloured with clustalx</li>
2260 <li>Choosing fonts without letter symbols defined causes
2261 exceptions and redraw errors</li>
2262 <li>Initial PCA plot view is not same as manually
2263 reconfigured view</li>
2264 <li>Grouped annotation graph label has incorrect line
2266 <li>Grouped annotation graph label display is corrupted
2267 for lots of labels</li>
2272 <div align="center">
2273 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2276 <td><em>Application</em>
2278 <li>Jalview Desktop News Reader</li>
2279 <li>Tweaked default layout of web services menu</li>
2280 <li>View/alignment association menu to enable user to
2281 easily specify which alignment a multi-structure view takes
2282 its colours/correspondences from</li>
2283 <li>Allow properties file location to be specified as URL</li>
2284 <li>Extend Jalview project to preserve associations
2285 between many alignment views and a single Jmol display</li>
2286 <li>Store annotation row height in Jalview project file</li>
2287 <li>Annotation row column label formatting attributes
2288 stored in project file</li>
2289 <li>Annotation row order for auto-calculated annotation
2290 rows preserved in Jalview project file</li>
2291 <li>Visual progress indication when Jalview state is
2292 saved using Desktop window menu</li>
2293 <li>Visual indication that command line arguments are
2294 still being processed</li>
2295 <li>Groovy script execution from URL</li>
2296 <li>Colour by annotation default min and max colours in
2298 <li>Automatically associate PDB files dragged onto an
2299 alignment with sequences that have high similarity and
2301 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2302 <li>'view structures' option to open many
2303 structures in same window</li>
2304 <li>Sort associated views menu option for tree panel</li>
2305 <li>Group all JABA and non-JABA services for a particular
2306 analysis function in its own submenu</li>
2307 </ul> <em>Applet</em>
2309 <li>Userdefined and autogenerated annotation rows for
2311 <li>Adjustment of alignment annotation pane height</li>
2312 <li>Annotation scrollbar for annotation panel</li>
2313 <li>Drag to reorder annotation rows in annotation panel</li>
2314 <li>'automaticScrolling' parameter</li>
2315 <li>Allow sequences with partial ID string matches to be
2316 annotated from GFF/Jalview features files</li>
2317 <li>Sequence logo annotation row in applet</li>
2318 <li>Absolute paths relative to host server in applet
2319 parameters are treated as such</li>
2320 <li>New in the JalviewLite javascript API:
2322 <li>JalviewLite.js javascript library</li>
2323 <li>Javascript callbacks for
2325 <li>Applet initialisation</li>
2326 <li>Sequence/alignment mouse-overs and selections</li>
2329 <li>scrollTo row and column alignment scrolling
2331 <li>Select sequence/alignment regions from javascript</li>
2332 <li>javascript structure viewer harness to pass
2333 messages between Jmol and Jalview when running as
2334 distinct applets</li>
2335 <li>sortBy method</li>
2336 <li>Set of applet and application examples shipped
2337 with documentation</li>
2338 <li>New example to demonstrate JalviewLite and Jmol
2339 javascript message exchange</li>
2341 </ul> <em>General</em>
2343 <li>Enable Jmol displays to be associated with multiple
2344 multiple alignments</li>
2345 <li>Option to automatically sort alignment with new tree</li>
2346 <li>User configurable link to enable redirects to a
2347 www.Jalview.org mirror</li>
2348 <li>Jmol colours option for Jmol displays</li>
2349 <li>Configurable newline string when writing alignment
2350 and other flat files</li>
2351 <li>Allow alignment annotation description lines to
2352 contain html tags</li>
2353 </ul> <em>Documentation and Development</em>
2355 <li>Add groovy test harness for bulk load testing to
2357 <li>Groovy script to load and align a set of sequences
2358 using a web service before displaying the result in the
2359 Jalview desktop</li>
2360 <li>Restructured javascript and applet api documentation</li>
2361 <li>Ant target to publish example html files with applet
2363 <li>Netbeans project for building Jalview from source</li>
2364 <li>ant task to create online javadoc for Jalview source</li>
2366 <td><em>Application</em>
2368 <li>User defined colourscheme throws exception when
2369 current built in colourscheme is saved as new scheme</li>
2370 <li>AlignFrame->Save in application pops up save
2371 dialog for valid filename/format</li>
2372 <li>Cannot view associated structure for UniProt sequence</li>
2373 <li>PDB file association breaks for UniProt sequence
2375 <li>Associate PDB from file dialog does not tell you
2376 which sequence is to be associated with the file</li>
2377 <li>Find All raises null pointer exception when query
2378 only matches sequence IDs</li>
2379 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2380 <li>Jalview project with Jmol views created with Jalview
2381 2.4 cannot be loaded</li>
2382 <li>Filetype associations not installed for webstart
2384 <li>Two or more chains in a single PDB file associated
2385 with sequences in different alignments do not get coloured
2386 by their associated sequence</li>
2387 <li>Visibility status of autocalculated annotation row
2388 not preserved when project is loaded</li>
2389 <li>Annotation row height and visibility attributes not
2390 stored in Jalview project</li>
2391 <li>Tree bootstraps are not preserved when saved as a
2392 Jalview project</li>
2393 <li>Envision2 workflow tooltips are corrupted</li>
2394 <li>Enabling show group conservation also enables colour
2395 by conservation</li>
2396 <li>Duplicate group associated conservation or consensus
2397 created on new view</li>
2398 <li>Annotation scrollbar not displayed after 'show
2399 all hidden annotation rows' option selected</li>
2400 <li>Alignment quality not updated after alignment
2401 annotation row is hidden then shown</li>
2402 <li>Preserve colouring of structures coloured by
2403 sequences in pre Jalview 2.7 projects</li>
2404 <li>Web service job parameter dialog is not laid out
2406 <li>Web services menu not refreshed after 'reset
2407 services' button is pressed in preferences</li>
2408 <li>Annotation off by one in Jalview v2_3 example project</li>
2409 <li>Structures imported from file and saved in project
2410 get name like jalview_pdb1234.txt when reloaded</li>
2411 <li>Jalview does not always retrieve progress of a JABAWS
2412 job execution in full once it is complete</li>
2413 </ul> <em>Applet</em>
2415 <li>Alignment height set incorrectly when lots of
2416 annotation rows are displayed</li>
2417 <li>Relative URLs in feature HTML text not resolved to
2419 <li>View follows highlighting does not work for positions
2421 <li><= shown as = in tooltip</li>
2422 <li>Export features raises exception when no features
2424 <li>Separator string used for serialising lists of IDs
2425 for javascript api is modified when separator string
2426 provided as parameter</li>
2427 <li>Null pointer exception when selecting tree leaves for
2428 alignment with no existing selection</li>
2429 <li>Relative URLs for datasources assumed to be relative
2430 to applet's codebase</li>
2431 <li>Status bar not updated after finished searching and
2432 search wraps around to first result</li>
2433 <li>StructureSelectionManager instance shared between
2434 several Jalview applets causes race conditions and memory
2436 <li>Hover tooltip and mouseover of position on structure
2437 not sent from Jmol in applet</li>
2438 <li>Certain sequences of javascript method calls to
2439 applet API fatally hang browser</li>
2440 </ul> <em>General</em>
2442 <li>View follows structure mouseover scrolls beyond
2443 position with wrapped view and hidden regions</li>
2444 <li>Find sequence position moves to wrong residue
2445 with/without hidden columns</li>
2446 <li>Sequence length given in alignment properties window
2448 <li>InvalidNumberFormat exceptions thrown when trying to
2449 import PDB like structure files</li>
2450 <li>Positional search results are only highlighted
2451 between user-supplied sequence start/end bounds</li>
2452 <li>End attribute of sequence is not validated</li>
2453 <li>Find dialog only finds first sequence containing a
2454 given sequence position</li>
2455 <li>Sequence numbering not preserved in MSF alignment
2457 <li>Jalview PDB file reader does not extract sequence
2458 from nucleotide chains correctly</li>
2459 <li>Structure colours not updated when tree partition
2460 changed in alignment</li>
2461 <li>Sequence associated secondary structure not correctly
2462 parsed in interleaved stockholm</li>
2463 <li>Colour by annotation dialog does not restore current
2465 <li>Hiding (nearly) all sequences doesn't work
2467 <li>Sequences containing lowercase letters are not
2468 properly associated with their pdb files</li>
2469 </ul> <em>Documentation and Development</em>
2471 <li>schemas/JalviewWsParamSet.xsd corrupted by
2472 ApplyCopyright tool</li>
2477 <div align="center">
2478 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2481 <td><em>Application</em>
2483 <li>New warning dialog when the Jalview Desktop cannot
2484 contact web services</li>
2485 <li>JABA service parameters for a preset are shown in
2486 service job window</li>
2487 <li>JABA Service menu entries reworded</li>
2491 <li>Modeller PIR IO broken - cannot correctly import a
2492 pir file emitted by Jalview</li>
2493 <li>Existing feature settings transferred to new
2494 alignment view created from cut'n'paste</li>
2495 <li>Improved test for mixed amino/nucleotide chains when
2496 parsing PDB files</li>
2497 <li>Consensus and conservation annotation rows
2498 occasionally become blank for all new windows</li>
2499 <li>Exception raised when right clicking above sequences
2500 in wrapped view mode</li>
2501 </ul> <em>Application</em>
2503 <li>multiple multiply aligned structure views cause cpu
2504 usage to hit 100% and computer to hang</li>
2505 <li>Web Service parameter layout breaks for long user
2506 parameter names</li>
2507 <li>Jaba service discovery hangs desktop if Jaba server
2514 <div align="center">
2515 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2518 <td><em>Application</em>
2520 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2521 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2524 <li>Web Services preference tab</li>
2525 <li>Analysis parameters dialog box and user defined
2527 <li>Improved speed and layout of Envision2 service menu</li>
2528 <li>Superpose structures using associated sequence
2530 <li>Export coordinates and projection as CSV from PCA
2532 </ul> <em>Applet</em>
2534 <li>enable javascript: execution by the applet via the
2535 link out mechanism</li>
2536 </ul> <em>Other</em>
2538 <li>Updated the Jmol Jalview interface to work with Jmol
2540 <li>The Jalview Desktop and JalviewLite applet now
2541 require Java 1.5</li>
2542 <li>Allow Jalview feature colour specification for GFF
2543 sequence annotation files</li>
2544 <li>New 'colour by label' keword in Jalview feature file
2545 type colour specification</li>
2546 <li>New Jalview Desktop Groovy API method that allows a
2547 script to check if it being run in an interactive session or
2548 in a batch operation from the Jalview command line</li>
2552 <li>clustalx colourscheme colours Ds preferentially when
2553 both D+E are present in over 50% of the column</li>
2554 </ul> <em>Application</em>
2556 <li>typo in AlignmentFrame->View->Hide->all but
2557 selected Regions menu item</li>
2558 <li>sequence fetcher replaces ',' for ';' when the ',' is
2559 part of a valid accession ID</li>
2560 <li>fatal OOM if object retrieved by sequence fetcher
2561 runs out of memory</li>
2562 <li>unhandled Out of Memory Error when viewing pca
2563 analysis results</li>
2564 <li>InstallAnywhere builds fail to launch on OS X java
2565 10.5 update 4 (due to apple Java 1.6 update)</li>
2566 <li>Installanywhere Jalview silently fails to launch</li>
2567 </ul> <em>Applet</em>
2569 <li>Jalview.getFeatureGroups() raises an
2570 ArrayIndexOutOfBoundsException if no feature groups are
2577 <div align="center">
2578 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2584 <li>Alignment prettyprinter doesn't cope with long
2586 <li>clustalx colourscheme colours Ds preferentially when
2587 both D+E are present in over 50% of the column</li>
2588 <li>nucleic acid structures retrieved from PDB do not
2589 import correctly</li>
2590 <li>More columns get selected than were clicked on when a
2591 number of columns are hidden</li>
2592 <li>annotation label popup menu not providing correct
2593 add/hide/show options when rows are hidden or none are
2595 <li>Stockholm format shown in list of readable formats,
2596 and parser copes better with alignments from RFAM.</li>
2597 <li>CSV output of consensus only includes the percentage
2598 of all symbols if sequence logo display is enabled</li>
2600 </ul> <em>Applet</em>
2602 <li>annotation panel disappears when annotation is
2604 </ul> <em>Application</em>
2606 <li>Alignment view not redrawn properly when new
2607 alignment opened where annotation panel is visible but no
2608 annotations are present on alignment</li>
2609 <li>pasted region containing hidden columns is
2610 incorrectly displayed in new alignment window</li>
2611 <li>Jalview slow to complete operations when stdout is
2612 flooded (fix is to close the Jalview console)</li>
2613 <li>typo in AlignmentFrame->View->Hide->all but
2614 selected Rregions menu item.</li>
2615 <li>inconsistent group submenu and Format submenu entry
2616 'Un' or 'Non'conserved</li>
2617 <li>Sequence feature settings are being shared by
2618 multiple distinct alignments</li>
2619 <li>group annotation not recreated when tree partition is
2621 <li>double click on group annotation to select sequences
2622 does not propagate to associated trees</li>
2623 <li>Mac OSX specific issues:
2625 <li>exception raised when mouse clicked on desktop
2626 window background</li>
2627 <li>Desktop menu placed on menu bar and application
2628 name set correctly</li>
2629 <li>sequence feature settings not wide enough for the
2630 save feature colourscheme button</li>
2639 <div align="center">
2640 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2643 <td><em>New Capabilities</em>
2645 <li>URL links generated from description line for
2646 regular-expression based URL links (applet and application)
2648 <li>Non-positional feature URL links are shown in link
2650 <li>Linked viewing of nucleic acid sequences and
2652 <li>Automatic Scrolling option in View menu to display
2653 the currently highlighted region of an alignment.</li>
2654 <li>Order an alignment by sequence length, or using the
2655 average score or total feature count for each sequence.</li>
2656 <li>Shading features by score or associated description</li>
2657 <li>Subdivide alignment and groups based on identity of
2658 selected subsequence (Make Groups from Selection).</li>
2659 <li>New hide/show options including Shift+Control+H to
2660 hide everything but the currently selected region.</li>
2661 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2662 </ul> <em>Application</em>
2664 <li>Fetch DB References capabilities and UI expanded to
2665 support retrieval from DAS sequence sources</li>
2666 <li>Local DAS Sequence sources can be added via the
2667 command line or via the Add local source dialog box.</li>
2668 <li>DAS Dbref and DbxRef feature types are parsed as
2669 database references and protein_name is parsed as
2670 description line (BioSapiens terms).</li>
2671 <li>Enable or disable non-positional feature and database
2672 references in sequence ID tooltip from View menu in
2674 <!-- <li>New hidden columns and rows and representatives capabilities
2675 in annotations file (in progress - not yet fully implemented)</li> -->
2676 <li>Group-associated consensus, sequence logos and
2677 conservation plots</li>
2678 <li>Symbol distributions for each column can be exported
2679 and visualized as sequence logos</li>
2680 <li>Optionally scale multi-character column labels to fit
2681 within each column of annotation row<!-- todo for applet -->
2683 <li>Optional automatic sort of associated alignment view
2684 when a new tree is opened.</li>
2685 <li>Jalview Java Console</li>
2686 <li>Better placement of desktop window when moving
2687 between different screens.</li>
2688 <li>New preference items for sequence ID tooltip and
2689 consensus annotation</li>
2690 <li>Client to submit sequences and IDs to Envision2
2692 <li><em>Vamsas Capabilities</em>
2694 <li>Improved VAMSAS synchronization (Jalview archive
2695 used to preserve views, structures, and tree display
2697 <li>Import of vamsas documents from disk or URL via
2699 <li>Sharing of selected regions between views and
2700 with other VAMSAS applications (Experimental feature!)</li>
2701 <li>Updated API to VAMSAS version 0.2</li>
2703 </ul> <em>Applet</em>
2705 <li>Middle button resizes annotation row height</li>
2708 <li>sortByTree (true/false) - automatically sort the
2709 associated alignment view by the tree when a new tree is
2711 <li>showTreeBootstraps (true/false) - show or hide
2712 branch bootstraps (default is to show them if available)</li>
2713 <li>showTreeDistances (true/false) - show or hide
2714 branch lengths (default is to show them if available)</li>
2715 <li>showUnlinkedTreeNodes (true/false) - indicate if
2716 unassociated nodes should be highlighted in the tree
2718 <li>heightScale and widthScale (1.0 or more) -
2719 increase the height or width of a cell in the alignment
2720 grid relative to the current font size.</li>
2723 <li>Non-positional features displayed in sequence ID
2725 </ul> <em>Other</em>
2727 <li>Features format: graduated colour definitions and
2728 specification of feature scores</li>
2729 <li>Alignment Annotations format: new keywords for group
2730 associated annotation (GROUP_REF) and annotation row display
2731 properties (ROW_PROPERTIES)</li>
2732 <li>XML formats extended to support graduated feature
2733 colourschemes, group associated annotation, and profile
2734 visualization settings.</li></td>
2737 <li>Source field in GFF files parsed as feature source
2738 rather than description</li>
2739 <li>Non-positional features are now included in sequence
2740 feature and gff files (controlled via non-positional feature
2741 visibility in tooltip).</li>
2742 <li>URL links generated for all feature links (bugfix)</li>
2743 <li>Added URL embedding instructions to features file
2745 <li>Codons containing ambiguous nucleotides translated as
2746 'X' in peptide product</li>
2747 <li>Match case switch in find dialog box works for both
2748 sequence ID and sequence string and query strings do not
2749 have to be in upper case to match case-insensitively.</li>
2750 <li>AMSA files only contain first column of
2751 multi-character column annotation labels</li>
2752 <li>Jalview Annotation File generation/parsing consistent
2753 with documentation (e.g. Stockholm annotation can be
2754 exported and re-imported)</li>
2755 <li>PDB files without embedded PDB IDs given a friendly
2757 <li>Find incrementally searches ID string matches as well
2758 as subsequence matches, and correctly reports total number
2762 <li>Better handling of exceptions during sequence
2764 <li>Dasobert generated non-positional feature URL
2765 link text excludes the start_end suffix</li>
2766 <li>DAS feature and source retrieval buttons disabled
2767 when fetch or registry operations in progress.</li>
2768 <li>PDB files retrieved from URLs are cached properly</li>
2769 <li>Sequence description lines properly shared via
2771 <li>Sequence fetcher fetches multiple records for all
2773 <li>Ensured that command line das feature retrieval
2774 completes before alignment figures are generated.</li>
2775 <li>Reduced time taken when opening file browser for
2777 <li>isAligned check prior to calculating tree, PCA or
2778 submitting an MSA to JNet now excludes hidden sequences.</li>
2779 <li>User defined group colours properly recovered
2780 from Jalview projects.</li>
2789 <div align="center">
2790 <strong>2.4.0.b2</strong><br> 28/10/2009
2795 <li>Experimental support for google analytics usage
2797 <li>Jalview privacy settings (user preferences and docs).</li>
2802 <li>Race condition in applet preventing startup in
2804 <li>Exception when feature created from selection beyond
2805 length of sequence.</li>
2806 <li>Allow synthetic PDB files to be imported gracefully</li>
2807 <li>Sequence associated annotation rows associate with
2808 all sequences with a given id</li>
2809 <li>Find function matches case-insensitively for sequence
2810 ID string searches</li>
2811 <li>Non-standard characters do not cause pairwise
2812 alignment to fail with exception</li>
2813 </ul> <em>Application Issues</em>
2815 <li>Sequences are now validated against EMBL database</li>
2816 <li>Sequence fetcher fetches multiple records for all
2818 </ul> <em>InstallAnywhere Issues</em>
2820 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2821 issue with installAnywhere mechanism)</li>
2822 <li>Command line launching of JARs from InstallAnywhere
2823 version (java class versioning error fixed)</li>
2830 <div align="center">
2831 <strong>2.4</strong><br> 27/8/2008
2834 <td><em>User Interface</em>
2836 <li>Linked highlighting of codon and amino acid from
2837 translation and protein products</li>
2838 <li>Linked highlighting of structure associated with
2839 residue mapping to codon position</li>
2840 <li>Sequence Fetcher provides example accession numbers
2841 and 'clear' button</li>
2842 <li>MemoryMonitor added as an option under Desktop's
2844 <li>Extract score function to parse whitespace separated
2845 numeric data in description line</li>
2846 <li>Column labels in alignment annotation can be centred.</li>
2847 <li>Tooltip for sequence associated annotation give name
2849 </ul> <em>Web Services and URL fetching</em>
2851 <li>JPred3 web service</li>
2852 <li>Prototype sequence search client (no public services
2854 <li>Fetch either seed alignment or full alignment from
2856 <li>URL Links created for matching database cross
2857 references as well as sequence ID</li>
2858 <li>URL Links can be created using regular-expressions</li>
2859 </ul> <em>Sequence Database Connectivity</em>
2861 <li>Retrieval of cross-referenced sequences from other
2863 <li>Generalised database reference retrieval and
2864 validation to all fetchable databases</li>
2865 <li>Fetch sequences from DAS sources supporting the
2866 sequence command</li>
2867 </ul> <em>Import and Export</em>
2868 <li>export annotation rows as CSV for spreadsheet import</li>
2869 <li>Jalview projects record alignment dataset associations,
2870 EMBL products, and cDNA sequence mappings</li>
2871 <li>Sequence Group colour can be specified in Annotation
2873 <li>Ad-hoc colouring of group in Annotation File using RGB
2874 triplet as name of colourscheme</li>
2875 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2877 <li>treenode binding for VAMSAS tree exchange</li>
2878 <li>local editing and update of sequences in VAMSAS
2879 alignments (experimental)</li>
2880 <li>Create new or select existing session to join</li>
2881 <li>load and save of vamsas documents</li>
2882 </ul> <em>Application command line</em>
2884 <li>-tree parameter to open trees (introduced for passing
2886 <li>-fetchfrom command line argument to specify nicknames
2887 of DAS servers to query for alignment features</li>
2888 <li>-dasserver command line argument to add new servers
2889 that are also automatically queried for features</li>
2890 <li>-groovy command line argument executes a given groovy
2891 script after all input data has been loaded and parsed</li>
2892 </ul> <em>Applet-Application data exchange</em>
2894 <li>Trees passed as applet parameters can be passed to
2895 application (when using "View in full
2896 application")</li>
2897 </ul> <em>Applet Parameters</em>
2899 <li>feature group display control parameter</li>
2900 <li>debug parameter</li>
2901 <li>showbutton parameter</li>
2902 </ul> <em>Applet API methods</em>
2904 <li>newView public method</li>
2905 <li>Window (current view) specific get/set public methods</li>
2906 <li>Feature display control methods</li>
2907 <li>get list of currently selected sequences</li>
2908 </ul> <em>New Jalview distribution features</em>
2910 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2911 <li>RELEASE file gives build properties for the latest
2912 Jalview release.</li>
2913 <li>Java 1.1 Applet build made easier and donotobfuscate
2914 property controls execution of obfuscator</li>
2915 <li>Build target for generating source distribution</li>
2916 <li>Debug flag for javacc</li>
2917 <li>.jalview_properties file is documented (slightly) in
2918 jalview.bin.Cache</li>
2919 <li>Continuous Build Integration for stable and
2920 development version of Application, Applet and source
2925 <li>selected region output includes visible annotations
2926 (for certain formats)</li>
2927 <li>edit label/displaychar contains existing label/char
2929 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2930 <li>shorter peptide product names from EMBL records</li>
2931 <li>Newick string generator makes compact representations</li>
2932 <li>bootstrap values parsed correctly for tree files with
2934 <li>pathological filechooser bug avoided by not allowing
2935 filenames containing a ':'</li>
2936 <li>Fixed exception when parsing GFF files containing
2937 global sequence features</li>
2938 <li>Alignment datasets are finalized only when number of
2939 references from alignment sequences goes to zero</li>
2940 <li>Close of tree branch colour box without colour
2941 selection causes cascading exceptions</li>
2942 <li>occasional negative imgwidth exceptions</li>
2943 <li>better reporting of non-fatal warnings to user when
2944 file parsing fails.</li>
2945 <li>Save works when Jalview project is default format</li>
2946 <li>Save as dialog opened if current alignment format is
2947 not a valid output format</li>
2948 <li>UniProt canonical names introduced for both das and
2950 <li>Histidine should be midblue (not pink!) in Zappo</li>
2951 <li>error messages passed up and output when data read
2953 <li>edit undo recovers previous dataset sequence when
2954 sequence is edited</li>
2955 <li>allow PDB files without pdb ID HEADER lines (like
2956 those generated by MODELLER) to be read in properly</li>
2957 <li>allow reading of JPred concise files as a normal
2959 <li>Stockholm annotation parsing and alignment properties
2960 import fixed for PFAM records</li>
2961 <li>Structure view windows have correct name in Desktop
2963 <li>annotation consisting of sequence associated scores
2964 can be read and written correctly to annotation file</li>
2965 <li>Aligned cDNA translation to aligned peptide works
2967 <li>Fixed display of hidden sequence markers and
2968 non-italic font for representatives in Applet</li>
2969 <li>Applet Menus are always embedded in applet window on
2971 <li>Newly shown features appear at top of stack (in
2973 <li>Annotations added via parameter not drawn properly
2974 due to null pointer exceptions</li>
2975 <li>Secondary structure lines are drawn starting from
2976 first column of alignment</li>
2977 <li>UniProt XML import updated for new schema release in
2979 <li>Sequence feature to sequence ID match for Features
2980 file is case-insensitive</li>
2981 <li>Sequence features read from Features file appended to
2982 all sequences with matching IDs</li>
2983 <li>PDB structure coloured correctly for associated views
2984 containing a sub-sequence</li>
2985 <li>PDB files can be retrieved by applet from Jar files</li>
2986 <li>feature and annotation file applet parameters
2987 referring to different directories are retrieved correctly</li>
2988 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2989 <li>Fixed application hang whilst waiting for
2990 splash-screen version check to complete</li>
2991 <li>Applet properly URLencodes input parameter values
2992 when passing them to the launchApp service</li>
2993 <li>display name and local features preserved in results
2994 retrieved from web service</li>
2995 <li>Visual delay indication for sequence retrieval and
2996 sequence fetcher initialisation</li>
2997 <li>updated Application to use DAS 1.53e version of
2998 dasobert DAS client</li>
2999 <li>Re-instated Full AMSA support and .amsa file
3001 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3009 <div align="center">
3010 <strong>2.3</strong><br> 9/5/07
3015 <li>Jmol 11.0.2 integration</li>
3016 <li>PDB views stored in Jalview XML files</li>
3017 <li>Slide sequences</li>
3018 <li>Edit sequence in place</li>
3019 <li>EMBL CDS features</li>
3020 <li>DAS Feature mapping</li>
3021 <li>Feature ordering</li>
3022 <li>Alignment Properties</li>
3023 <li>Annotation Scores</li>
3024 <li>Sort by scores</li>
3025 <li>Feature/annotation editing in applet</li>
3030 <li>Headless state operation in 2.2.1</li>
3031 <li>Incorrect and unstable DNA pairwise alignment</li>
3032 <li>Cut and paste of sequences with annotation</li>
3033 <li>Feature group display state in XML</li>
3034 <li>Feature ordering in XML</li>
3035 <li>blc file iteration selection using filename # suffix</li>
3036 <li>Stockholm alignment properties</li>
3037 <li>Stockhom alignment secondary structure annotation</li>
3038 <li>2.2.1 applet had no feature transparency</li>
3039 <li>Number pad keys can be used in cursor mode</li>
3040 <li>Structure Viewer mirror image resolved</li>
3047 <div align="center">
3048 <strong>2.2.1</strong><br> 12/2/07
3053 <li>Non standard characters can be read and displayed
3054 <li>Annotations/Features can be imported/exported to the
3056 <li>Applet allows editing of sequence/annotation/group
3057 name & description
3058 <li>Preference setting to display sequence name in
3060 <li>Annotation file format extended to allow
3061 Sequence_groups to be defined
3062 <li>Default opening of alignment overview panel can be
3063 specified in preferences
3064 <li>PDB residue numbering annotation added to associated
3070 <li>Applet crash under certain Linux OS with Java 1.6
3072 <li>Annotation file export / import bugs fixed
3073 <li>PNG / EPS image output bugs fixed
3079 <div align="center">
3080 <strong>2.2</strong><br> 27/11/06
3085 <li>Multiple views on alignment
3086 <li>Sequence feature editing
3087 <li>"Reload" alignment
3088 <li>"Save" to current filename
3089 <li>Background dependent text colour
3090 <li>Right align sequence ids
3091 <li>User-defined lower case residue colours
3094 <li>Menu item accelerator keys
3095 <li>Control-V pastes to current alignment
3096 <li>Cancel button for DAS Feature Fetching
3097 <li>PCA and PDB Viewers zoom via mouse roller
3098 <li>User-defined sub-tree colours and sub-tree selection
3100 <li>'New Window' button on the 'Output to Text box'
3105 <li>New memory efficient Undo/Redo System
3106 <li>Optimised symbol lookups and conservation/consensus
3108 <li>Region Conservation/Consensus recalculated after
3110 <li>Fixed Remove Empty Columns Bug (empty columns at end
3112 <li>Slowed DAS Feature Fetching for increased robustness.
3114 <li>Made angle brackets in ASCII feature descriptions
3116 <li>Re-instated Zoom function for PCA
3117 <li>Sequence descriptions conserved in web service
3119 <li>UniProt ID discoverer uses any word separated by
3121 <li>WsDbFetch query/result association resolved
3122 <li>Tree leaf to sequence mapping improved
3123 <li>Smooth fonts switch moved to FontChooser dialog box.
3130 <div align="center">
3131 <strong>2.1.1</strong><br> 12/9/06
3136 <li>Copy consensus sequence to clipboard</li>
3141 <li>Image output - rightmost residues are rendered if
3142 sequence id panel has been resized</li>
3143 <li>Image output - all offscreen group boundaries are
3145 <li>Annotation files with sequence references - all
3146 elements in file are relative to sequence position</li>
3147 <li>Mac Applet users can use Alt key for group editing</li>
3153 <div align="center">
3154 <strong>2.1</strong><br> 22/8/06
3159 <li>MAFFT Multiple Alignment in default Web Service list</li>
3160 <li>DAS Feature fetching</li>
3161 <li>Hide sequences and columns</li>
3162 <li>Export Annotations and Features</li>
3163 <li>GFF file reading / writing</li>
3164 <li>Associate structures with sequences from local PDB
3166 <li>Add sequences to exisiting alignment</li>
3167 <li>Recently opened files / URL lists</li>
3168 <li>Applet can launch the full application</li>
3169 <li>Applet has transparency for features (Java 1.2
3171 <li>Applet has user defined colours parameter</li>
3172 <li>Applet can load sequences from parameter
3173 "sequence<em>x</em>"
3179 <li>Redundancy Panel reinstalled in the Applet</li>
3180 <li>Monospaced font - EPS / rescaling bug fixed</li>
3181 <li>Annotation files with sequence references bug fixed</li>
3187 <div align="center">
3188 <strong>2.08.1</strong><br> 2/5/06
3193 <li>Change case of selected region from Popup menu</li>
3194 <li>Choose to match case when searching</li>
3195 <li>Middle mouse button and mouse movement can compress /
3196 expand the visible width and height of the alignment</li>
3201 <li>Annotation Panel displays complete JNet results</li>
3207 <div align="center">
3208 <strong>2.08b</strong><br> 18/4/06
3214 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3215 <li>Righthand label on wrapped alignments shows correct
3222 <div align="center">
3223 <strong>2.08</strong><br> 10/4/06
3228 <li>Editing can be locked to the selection area</li>
3229 <li>Keyboard editing</li>
3230 <li>Create sequence features from searches</li>
3231 <li>Precalculated annotations can be loaded onto
3233 <li>Features file allows grouping of features</li>
3234 <li>Annotation Colouring scheme added</li>
3235 <li>Smooth fonts off by default - Faster rendering</li>
3236 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3241 <li>Drag & Drop fixed on Linux</li>
3242 <li>Jalview Archive file faster to load/save, sequence
3243 descriptions saved.</li>
3249 <div align="center">
3250 <strong>2.07</strong><br> 12/12/05
3255 <li>PDB Structure Viewer enhanced</li>
3256 <li>Sequence Feature retrieval and display enhanced</li>
3257 <li>Choose to output sequence start-end after sequence
3258 name for file output</li>
3259 <li>Sequence Fetcher WSDBFetch@EBI</li>
3260 <li>Applet can read feature files, PDB files and can be
3261 used for HTML form input</li>
3266 <li>HTML output writes groups and features</li>
3267 <li>Group editing is Control and mouse click</li>
3268 <li>File IO bugs</li>
3274 <div align="center">
3275 <strong>2.06</strong><br> 28/9/05
3280 <li>View annotations in wrapped mode</li>
3281 <li>More options for PCA viewer</li>
3286 <li>GUI bugs resolved</li>
3287 <li>Runs with -nodisplay from command line</li>
3293 <div align="center">
3294 <strong>2.05b</strong><br> 15/9/05
3299 <li>Choose EPS export as lineart or text</li>
3300 <li>Jar files are executable</li>
3301 <li>Can read in Uracil - maps to unknown residue</li>
3306 <li>Known OutOfMemory errors give warning message</li>
3307 <li>Overview window calculated more efficiently</li>
3308 <li>Several GUI bugs resolved</li>
3314 <div align="center">
3315 <strong>2.05</strong><br> 30/8/05
3320 <li>Edit and annotate in "Wrapped" view</li>
3325 <li>Several GUI bugs resolved</li>
3331 <div align="center">
3332 <strong>2.04</strong><br> 24/8/05
3337 <li>Hold down mouse wheel & scroll to change font
3343 <li>Improved JPred client reliability</li>
3344 <li>Improved loading of Jalview files</li>
3350 <div align="center">
3351 <strong>2.03</strong><br> 18/8/05
3356 <li>Set Proxy server name and port in preferences</li>
3357 <li>Multiple URL links from sequence ids</li>
3358 <li>User Defined Colours can have a scheme name and added
3360 <li>Choose to ignore gaps in consensus calculation</li>
3361 <li>Unix users can set default web browser</li>
3362 <li>Runs without GUI for batch processing</li>
3363 <li>Dynamically generated Web Service Menus</li>
3368 <li>InstallAnywhere download for Sparc Solaris</li>
3374 <div align="center">
3375 <strong>2.02</strong><br> 18/7/05
3381 <li>Copy & Paste order of sequences maintains
3382 alignment order.</li>
3388 <div align="center">
3389 <strong>2.01</strong><br> 12/7/05
3394 <li>Use delete key for deleting selection.</li>
3395 <li>Use Mouse wheel to scroll sequences.</li>
3396 <li>Help file updated to describe how to add alignment
3398 <li>Version and build date written to build properties
3400 <li>InstallAnywhere installation will check for updates
3401 at launch of Jalview.</li>
3406 <li>Delete gaps bug fixed.</li>
3407 <li>FileChooser sorts columns.</li>
3408 <li>Can remove groups one by one.</li>
3409 <li>Filechooser icons installed.</li>
3410 <li>Finder ignores return character when searching.
3411 Return key will initiate a search.<br>
3418 <div align="center">
3419 <strong>2.0</strong><br> 20/6/05
3424 <li>New codebase</li>