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.2.10.3">2.10.3</a><br />
74 <em>10/10/2017</em></strong>
77 <td><div align="left">
81 <!-- JAL-2446 -->Faster and more efficient management and
82 rendering of sequence features
86 <td><div align="left">
89 <li><!-- JAL-2728 -->Protein annotation panel too high in CDS/Protein view
95 <td width="60" nowrap>
97 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
98 <em>7/9/2017</em></strong>
101 <td><div align="left">
105 <!-- JAL-2588 -->Show gaps in overview window by colouring
106 in grey (sequences used to be coloured grey, and gaps were
110 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
114 <!-- JAL-2587 -->Overview updates immediately on increase
115 in size and progress bar shown as higher resolution
116 overview is recalculated
121 <td><div align="left">
125 <!-- JAL-2664 -->Overview window redraws every hidden
126 column region row by row
129 <!-- JAL-2681 -->duplicate protein sequences shown after
130 retrieving Ensembl crossrefs for sequences from Uniprot
133 <!-- JAL-2603 -->Overview window throws NPE if show boxes
134 format setting is unticked
137 <!-- JAL-2610 -->Groups are coloured wrongly in overview
138 if group has show boxes format setting unticked
141 <!-- JAL-2672,JAL-2665 -->Redraw problems when
142 autoscrolling whilst dragging current selection group to
143 include sequences and columns not currently displayed
146 <!-- JAL-2691 -->Not all chains are mapped when multimeric
147 assemblies are imported via CIF file
150 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
151 displayed when threshold or conservation colouring is also
155 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
159 <!-- JAL-2673 -->Jalview continues to scroll after
160 dragging a selected region off the visible region of the
164 <!-- JAL-2724 -->Cannot apply annotation based
165 colourscheme to all groups in a view
168 <!-- JAL-2511 -->IDs don't line up with sequences
169 initially after font size change using the Font chooser or
176 <td width="60" nowrap>
178 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
181 <td><div align="left">
182 <em>Calculations</em>
186 <!-- JAL-1933 -->Occupancy annotation row shows number of
187 ungapped positions in each column of the alignment.
190 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
191 a calculation dialog box
194 <!-- JAL-2379 -->Revised implementation of PCA for speed
195 and memory efficiency (~30x faster)
198 <!-- JAL-2403 -->Revised implementation of sequence
199 similarity scores as used by Tree, PCA, Shading Consensus
200 and other calculations
203 <!-- JAL-2416 -->Score matrices are stored as resource
204 files within the Jalview codebase
207 <!-- JAL-2500 -->Trees computed on Sequence Feature
208 Similarity may have different topology due to increased
215 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
216 model for alignments and groups
219 <!-- JAL-384 -->Custom shading schemes created via groovy
226 <!-- JAL-2526 -->Efficiency improvements for interacting
227 with alignment and overview windows
230 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
234 <!-- JAL-2388 -->Hidden columns and sequences can be
238 <!-- JAL-2611 -->Click-drag in visible area allows fine
239 adjustment of visible position
243 <em>Data import/export</em>
246 <!-- JAL-2535 -->Posterior probability annotation from
247 Stockholm files imported as sequence associated annotation
250 <!-- JAL-2507 -->More robust per-sequence positional
251 annotation input/output via stockholm flatfile
254 <!-- JAL-2533 -->Sequence names don't include file
255 extension when importing structure files without embedded
256 names or PDB accessions
259 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
260 format sequence substitution matrices
263 <em>User Interface</em>
266 <!-- JAL-2447 --> Experimental Features Checkbox in
267 Desktop's Tools menu to hide or show untested features in
271 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
272 via Overview or sequence motif search operations
275 <!-- JAL-2547 -->Amend sequence features dialog box can be
276 opened by double clicking gaps within sequence feature
280 <!-- JAL-1476 -->Status bar message shown when not enough
281 aligned positions were available to create a 3D structure
285 <em>3D Structure</em>
288 <!-- JAL-2430 -->Hidden regions in alignment views are not
289 coloured in linked structure views
292 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
293 file-based command exchange
296 <!-- JAL-2375 -->Structure chooser automatically shows
297 Cached Structures rather than querying the PDBe if
298 structures are already available for sequences
301 <!-- JAL-2520 -->Structures imported via URL are cached in
302 the Jalview project rather than downloaded again when the
306 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
307 to transfer Chimera's structure attributes as Jalview
308 features, and vice-versa (<strong>Experimental
312 <em>Web Services</em>
315 <!-- JAL-2549 -->Updated JABAWS client to v2.2
318 <!-- JAL-2335 -->Filter non-standard amino acids and
319 nucleotides when submitting to AACon and other MSA
323 <!-- JAL-2316, -->URLs for viewing database
324 cross-references provided by identifiers.org and the
332 <!-- JAL-2344 -->FileFormatI interface for describing and
333 identifying file formats (instead of String constants)
336 <!-- JAL-2228 -->FeatureCounter script refactored for
337 efficiency when counting all displayed features (not
338 backwards compatible with 2.10.1)
341 <em>Example files</em>
344 <!-- JAL-2631 -->Graduated feature colour style example
345 included in the example feature file
348 <em>Documentation</em>
351 <!-- JAL-2339 -->Release notes reformatted for readability
352 with the built-in Java help viewer
355 <!-- JAL-1644 -->Find documentation updated with 'search
356 sequence description' option
362 <!-- JAL-2485, -->External service integration tests for
363 Uniprot REST Free Text Search Client
366 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
369 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
374 <td><div align="left">
375 <em>Calculations</em>
378 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
379 matrix - C->R should be '-3'<br />Old matrix restored
380 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
382 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
383 Jalview's treatment of gaps in PCA and substitution matrix
384 based Tree calculations.<br /> <br />In earlier versions
385 of Jalview, gaps matching gaps were penalised, and gaps
386 matching non-gaps penalised even more. In the PCA
387 calculation, gaps were actually treated as non-gaps - so
388 different costs were applied, which meant Jalview's PCAs
389 were different to those produced by SeqSpace.<br />Jalview
390 now treats gaps in the same way as SeqSpace (ie it scores
391 them as 0). <br /> <br />Enter the following in the
392 Groovy console to restore pre-2.10.2 behaviour:<br />
393 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
394 // for 2.10.1 mode <br />
395 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
396 // to restore 2.10.2 mode <br /> <br /> <em>Note:
397 these settings will affect all subsequent tree and PCA
398 calculations (not recommended)</em></li>
400 <!-- JAL-2424 -->Fixed off-by-one bug that affected
401 scaling of branch lengths for trees computed using
402 Sequence Feature Similarity.
405 <!-- JAL-2377 -->PCA calculation could hang when
406 generating output report when working with highly
410 <!-- JAL-2544 --> Sort by features includes features to
411 right of selected region when gaps present on right-hand
415 <em>User Interface</em>
418 <!-- JAL-2346 -->Reopening Colour by annotation dialog
419 doesn't reselect a specific sequence's associated
420 annotation after it was used for colouring a view
423 <!-- JAL-2419 -->Current selection lost if popup menu
424 opened on a region of alignment without groups
427 <!-- JAL-2374 -->Popup menu not always shown for regions
428 of an alignment with overlapping groups
431 <!-- JAL-2310 -->Finder double counts if both a sequence's
432 name and description match
435 <!-- JAL-2370 -->Hiding column selection containing two
436 hidden regions results in incorrect hidden regions
439 <!-- JAL-2386 -->'Apply to all groups' setting when
440 changing colour does not apply Conservation slider value
444 <!-- JAL-2373 -->Percentage identity and conservation menu
445 items do not show a tick or allow shading to be disabled
448 <!-- JAL-2385 -->Conservation shading or PID threshold
449 lost when base colourscheme changed if slider not visible
452 <!-- JAL-2547 -->Sequence features shown in tooltip for
453 gaps before start of features
456 <!-- JAL-2623 -->Graduated feature colour threshold not
457 restored to UI when feature colour is edited
460 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
461 a time when scrolling vertically in wrapped mode.
464 <!-- JAL-2630 -->Structure and alignment overview update
465 as graduate feature colour settings are modified via the
469 <!-- JAL-2034 -->Overview window doesn't always update
470 when a group defined on the alignment is resized
473 <!-- JAL-2605 -->Mouseovers on left/right scale region in
474 wrapped view result in positional status updates
478 <!-- JAL-2563 -->Status bar doesn't show position for
479 ambiguous amino acid and nucleotide symbols
482 <!-- JAL-2602 -->Copy consensus sequence failed if
483 alignment included gapped columns
486 <!-- JAL-2473 -->Minimum size set for Jalview windows so
487 widgets don't permanently disappear
490 <!-- JAL-2503 -->Cannot select or filter quantitative
491 annotation that are shown only as column labels (e.g.
492 T-Coffee column reliability scores)
495 <!-- JAL-2594 -->Exception thrown if trying to create a
496 sequence feature on gaps only
499 <!-- JAL-2504 -->Features created with 'New feature'
500 button from a Find inherit previously defined feature type
501 rather than the Find query string
504 <!-- JAL-2423 -->incorrect title in output window when
505 exporting tree calculated in Jalview
508 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
509 and then revealing them reorders sequences on the
513 <!-- JAL-964 -->Group panel in sequence feature settings
514 doesn't update to reflect available set of groups after
515 interactively adding or modifying features
518 <!-- JAL-2225 -->Sequence Database chooser unusable on
522 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
523 only excluded gaps in current sequence and ignored
530 <!-- JAL-2421 -->Overview window visible region moves
531 erratically when hidden rows or columns are present
534 <!-- JAL-2362 -->Per-residue colourschemes applied via the
535 Structure Viewer's colour menu don't correspond to
539 <!-- JAL-2405 -->Protein specific colours only offered in
540 colour and group colour menu for protein alignments
543 <!-- JAL-2385 -->Colour threshold slider doesn't update to
544 reflect currently selected view or group's shading
548 <!-- JAL-2624 -->Feature colour thresholds not respected
549 when rendered on overview and structures when opacity at
553 <!-- JAL-2589 -->User defined gap colour not shown in
554 overview when features overlaid on alignment
557 <em>Data import/export</em>
560 <!-- JAL-2576 -->Very large alignments take a long time to
564 <!-- JAL-2507 -->Per-sequence RNA secondary structures
565 added after a sequence was imported are not written to
569 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
570 when importing RNA secondary structure via Stockholm
573 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
574 not shown in correct direction for simple pseudoknots
577 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
578 with lightGray or darkGray via features file (but can
582 <!-- JAL-2383 -->Above PID colour threshold not recovered
583 when alignment view imported from project
586 <!-- JAL-2520,JAL-2465 -->No mappings generated between
587 structure and sequences extracted from structure files
588 imported via URL and viewed in Jmol
591 <!-- JAL-2520 -->Structures loaded via URL are saved in
592 Jalview Projects rather than fetched via URL again when
593 the project is loaded and the structure viewed
596 <em>Web Services</em>
599 <!-- JAL-2519 -->EnsemblGenomes example failing after
600 release of Ensembl v.88
603 <!-- JAL-2366 -->Proxy server address and port always
604 appear enabled in Preferences->Connections
607 <!-- JAL-2461 -->DAS registry not found exceptions
608 removed from console output
611 <!-- JAL-2582 -->Cannot retrieve protein products from
612 Ensembl by Peptide ID
615 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
616 created from SIFTs, and spurious 'Couldn't open structure
617 in Chimera' errors raised after April 2017 update (problem
618 due to 'null' string rather than empty string used for
619 residues with no corresponding PDB mapping).
622 <em>Application UI</em>
625 <!-- JAL-2361 -->User Defined Colours not added to Colour
629 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
630 case' residues (button in colourscheme editor debugged and
631 new documentation and tooltips added)
634 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
635 doesn't restore group-specific text colour thresholds
638 <!-- JAL-2243 -->Feature settings panel does not update as
639 new features are added to alignment
642 <!-- JAL-2532 -->Cancel in feature settings reverts
643 changes to feature colours via the Amend features dialog
646 <!-- JAL-2506 -->Null pointer exception when attempting to
647 edit graduated feature colour via amend features dialog
651 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
652 selection menu changes colours of alignment views
655 <!-- JAL-2426 -->Spurious exceptions in console raised
656 from alignment calculation workers after alignment has
660 <!-- JAL-1608 -->Typo in selection popup menu - Create
661 groups now 'Create Group'
664 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
665 Create/Undefine group doesn't always work
668 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
669 shown again after pressing 'Cancel'
672 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
673 adjusts start position in wrap mode
676 <!-- JAL-2563 -->Status bar doesn't show positions for
677 ambiguous amino acids
680 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
681 CDS/Protein view after CDS sequences added for aligned
685 <!-- JAL-2592 -->User defined colourschemes called 'User
686 Defined' don't appear in Colours menu
692 <!-- JAL-2468 -->Switching between Nucleotide and Protein
693 score models doesn't always result in an updated PCA plot
696 <!-- JAL-2442 -->Features not rendered as transparent on
697 overview or linked structure view
700 <!-- JAL-2372 -->Colour group by conservation doesn't
704 <!-- JAL-2517 -->Hitting Cancel after applying
705 user-defined colourscheme doesn't restore original
712 <!-- JAL-2314 -->Unit test failure:
713 jalview.ws.jabaws.RNAStructExportImport setup fails
716 <!-- JAL-2307 -->Unit test failure:
717 jalview.ws.sifts.SiftsClientTest due to compatibility
718 problems with deep array comparison equality asserts in
719 successive versions of TestNG
722 <!-- JAL-2479 -->Relocated StructureChooserTest and
723 ParameterUtilsTest Unit tests to Network suite
726 <em>New Known Issues</em>
729 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
730 phase after a sequence motif find operation
733 <!-- JAL-2550 -->Importing annotation file with rows
734 containing just upper and lower case letters are
735 interpreted as WUSS RNA secondary structure symbols
738 <!-- JAL-2590 -->Cannot load and display Newick trees
739 reliably from eggnog Ortholog database
742 <!-- JAL-2468 -->Status bar shows 'Marked x columns
743 containing features of type Highlight' when 'B' is pressed
744 to mark columns containing highlighted regions.
747 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
748 doesn't always add secondary structure annotation.
753 <td width="60" nowrap>
755 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
758 <td><div align="left">
762 <!-- JAL-98 -->Improved memory usage: sparse arrays used
763 for all consensus calculations
766 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
769 <li>Updated Jalview's Certum code signing certificate
775 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
776 set of database cross-references, sorted alphabetically
779 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
780 from database cross references. Users with custom links
781 will receive a <a href="webServices/urllinks.html#warning">warning
782 dialog</a> asking them to update their preferences.
785 <!-- JAL-2287-->Cancel button and escape listener on
786 dialog warning user about disconnecting Jalview from a
790 <!-- JAL-2320-->Jalview's Chimera control window closes if
791 the Chimera it is connected to is shut down
794 <!-- JAL-1738-->New keystroke (B) and Select highlighted
795 columns menu item to mark columns containing highlighted
796 regions (e.g. from structure selections or results of a
800 <!-- JAL-2284-->Command line option for batch-generation
801 of HTML pages rendering alignment data with the BioJS
811 <!-- JAL-2286 -->Columns with more than one modal residue
812 are not coloured or thresholded according to percent
813 identity (first observed in Jalview 2.8.2)
816 <!-- JAL-2301 -->Threonine incorrectly reported as not
820 <!-- JAL-2318 -->Updates to documentation pages (above PID
821 threshold, amino acid properties)
824 <!-- JAL-2292 -->Lower case residues in sequences are not
825 reported as mapped to residues in a structure file in the
829 <!--JAL-2324 -->Identical features with non-numeric scores
830 could be added multiple times to a sequence
833 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
834 bond features shown as two highlighted residues rather
835 than a range in linked structure views, and treated
836 correctly when selecting and computing trees from features
839 <!-- JAL-2281-->Custom URL links for database
840 cross-references are matched to database name regardless
848 <!-- JAL-2282-->Custom URL links for specific database
849 names without regular expressions also offer links from
853 <!-- JAL-2315-->Removing a single configured link in the
854 URL links pane in Connections preferences doesn't actually
855 update Jalview configuration
858 <!-- JAL-2272-->CTRL-Click on a selected region to open
859 the alignment area popup menu doesn't work on El-Capitan
862 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
863 files with similarly named sequences if dropped onto the
867 <!-- JAL-2312 -->Additional mappings are shown for PDB
868 entries where more chains exist in the PDB accession than
869 are reported in the SIFTS file
872 <!-- JAL-2317-->Certain structures do not get mapped to
873 the structure view when displayed with Chimera
876 <!-- JAL-2317-->No chains shown in the Chimera view
877 panel's View->Show Chains submenu
880 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
881 work for wrapped alignment views
884 <!--JAL-2197 -->Rename UI components for running JPred
885 predictions from 'JNet' to 'JPred'
888 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
889 corrupted when annotation panel vertical scroll is not at
893 <!--JAL-2332 -->Attempting to view structure for Hen
894 lysozyme results in a PDB Client error dialog box
897 <!-- JAL-2319 -->Structure View's mapping report switched
898 ranges for PDB and sequence for SIFTS
901 SIFTS 'Not_Observed' residues mapped to non-existant
905 <!-- <em>New Known Issues</em>
912 <td width="60" nowrap>
914 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
915 <em>25/10/2016</em></strong>
918 <td><em>Application</em>
920 <li>3D Structure chooser opens with 'Cached structures'
921 view if structures already loaded</li>
922 <li>Progress bar reports models as they are loaded to
929 <li>Colour by conservation always enabled and no tick
930 shown in menu when BLOSUM or PID shading applied</li>
931 <li>FER1_ARATH and FER2_ARATH labels were switched in
932 example sequences/projects/trees</li>
936 <li>Jalview projects with views of local PDB structure
937 files saved on Windows cannot be opened on OSX</li>
938 <li>Multiple structure views can be opened and superposed
939 without timeout for structures with multiple models or
940 multiple sequences in alignment</li>
941 <li>Cannot import or associated local PDB files without a
942 PDB ID HEADER line</li>
943 <li>RMSD is not output in Jmol console when superposition
945 <li>Drag and drop of URL from Browser fails for Linux and
946 OSX versions earlier than El Capitan</li>
947 <li>ENA client ignores invalid content from ENA server</li>
948 <li>Exceptions are not raised in console when ENA client
949 attempts to fetch non-existent IDs via Fetch DB Refs UI
951 <li>Exceptions are not raised in console when a new view
952 is created on the alignment</li>
953 <li>OSX right-click fixed for group selections: CMD-click
954 to insert/remove gaps in groups and CTRL-click to open group
957 <em>Build and deployment</em>
959 <li>URL link checker now copes with multi-line anchor
962 <em>New Known Issues</em>
964 <li>Drag and drop from URL links in browsers do not work
971 <td width="60" nowrap>
973 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
979 <!-- JAL-2124 -->Updated Spanish translations.
982 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
983 for importing structure data to Jalview. Enables mmCIF and
987 <!-- JAL-192 --->Alignment ruler shows positions relative to
991 <!-- JAL-2202 -->Position/residue shown in status bar when
992 mousing over sequence associated annotation
995 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
999 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
1000 '()', canonical '[]' and invalid '{}' base pair populations
1004 <!-- JAL-2092 -->Feature settings popup menu options for
1005 showing or hiding columns containing a feature
1008 <!-- JAL-1557 -->Edit selected group by double clicking on
1009 group and sequence associated annotation labels
1012 <!-- JAL-2236 -->Sequence name added to annotation label in
1013 select/hide columns by annotation and colour by annotation
1017 </ul> <em>Application</em>
1020 <!-- JAL-2050-->Automatically hide introns when opening a
1021 gene/transcript view
1024 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
1028 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
1029 structure mappings with the EMBL-EBI PDBe SIFTS database
1032 <!-- JAL-2079 -->Updated download sites used for Rfam and
1033 Pfam sources to xfam.org
1036 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
1039 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
1040 over sequences in Jalview
1043 <!-- JAL-2027-->Support for reverse-complement coding
1044 regions in ENA and EMBL
1047 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1048 for record retrieval via ENA rest API
1051 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1055 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1056 groovy script execution
1059 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1060 alignment window's Calculate menu
1063 <!-- JAL-1812 -->Allow groovy scripts that call
1064 Jalview.getAlignFrames() to run in headless mode
1067 <!-- JAL-2068 -->Support for creating new alignment
1068 calculation workers from groovy scripts
1071 <!-- JAL-1369 --->Store/restore reference sequence in
1075 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1076 associations are now saved/restored from project
1079 <!-- JAL-1993 -->Database selection dialog always shown
1080 before sequence fetcher is opened
1083 <!-- JAL-2183 -->Double click on an entry in Jalview's
1084 database chooser opens a sequence fetcher
1087 <!-- JAL-1563 -->Free-text search client for UniProt using
1088 the UniProt REST API
1091 <!-- JAL-2168 -->-nonews command line parameter to prevent
1092 the news reader opening
1095 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1096 querying stored in preferences
1099 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1103 <!-- JAL-1977-->Tooltips shown on database chooser
1106 <!-- JAL-391 -->Reverse complement function in calculate
1107 menu for nucleotide sequences
1110 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1111 and feature counts preserves alignment ordering (and
1112 debugged for complex feature sets).
1115 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1116 viewing structures with Jalview 2.10
1119 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1120 genome, transcript CCDS and gene ids via the Ensembl and
1121 Ensembl Genomes REST API
1124 <!-- JAL-2049 -->Protein sequence variant annotation
1125 computed for 'sequence_variant' annotation on CDS regions
1129 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1133 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1134 Ref Fetcher fails to match, or otherwise updates sequence
1135 data from external database records.
1138 <!-- JAL-2154 -->Revised Jalview Project format for
1139 efficient recovery of sequence coding and alignment
1140 annotation relationships.
1142 </ul> <!-- <em>Applet</em>
1153 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1157 <!-- JAL-2018-->Export features in Jalview format (again)
1158 includes graduated colourschemes
1161 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1162 working with big alignments and lots of hidden columns
1165 <!-- JAL-2053-->Hidden column markers not always rendered
1166 at right of alignment window
1169 <!-- JAL-2067 -->Tidied up links in help file table of
1173 <!-- JAL-2072 -->Feature based tree calculation not shown
1177 <!-- JAL-2075 -->Hidden columns ignored during feature
1178 based tree calculation
1181 <!-- JAL-2065 -->Alignment view stops updating when show
1182 unconserved enabled for group on alignment
1185 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1189 <!-- JAL-2146 -->Alignment column in status incorrectly
1190 shown as "Sequence position" when mousing over
1194 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1195 hidden columns present
1198 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1199 user created annotation added to alignment
1202 <!-- JAL-1841 -->RNA Structure consensus only computed for
1203 '()' base pair annotation
1206 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1207 in zero scores for all base pairs in RNA Structure
1211 <!-- JAL-2174-->Extend selection with columns containing
1215 <!-- JAL-2275 -->Pfam format writer puts extra space at
1216 beginning of sequence
1219 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1223 <!-- JAL-2238 -->Cannot create groups on an alignment from
1224 from a tree when t-coffee scores are shown
1227 <!-- JAL-1836,1967 -->Cannot import and view PDB
1228 structures with chains containing negative resnums (4q4h)
1231 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1235 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1236 to Clustal, PIR and PileUp output
1239 <!-- JAL-2008 -->Reordering sequence features that are
1240 not visible causes alignment window to repaint
1243 <!-- JAL-2006 -->Threshold sliders don't work in
1244 graduated colour and colour by annotation row for e-value
1245 scores associated with features and annotation rows
1248 <!-- JAL-1797 -->amino acid physicochemical conservation
1249 calculation should be case independent
1252 <!-- JAL-2173 -->Remove annotation also updates hidden
1256 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1257 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1258 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1261 <!-- JAL-2065 -->Null pointer exceptions and redraw
1262 problems when reference sequence defined and 'show
1263 non-conserved' enabled
1266 <!-- JAL-1306 -->Quality and Conservation are now shown on
1267 load even when Consensus calculation is disabled
1270 <!-- JAL-1932 -->Remove right on penultimate column of
1271 alignment does nothing
1274 <em>Application</em>
1277 <!-- JAL-1552-->URLs and links can't be imported by
1278 drag'n'drop on OSX when launched via webstart (note - not
1279 yet fixed for El Capitan)
1282 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1283 output when running on non-gb/us i18n platforms
1286 <!-- JAL-1944 -->Error thrown when exporting a view with
1287 hidden sequences as flat-file alignment
1290 <!-- JAL-2030-->InstallAnywhere distribution fails when
1294 <!-- JAL-2080-->Jalview very slow to launch via webstart
1295 (also hotfix for 2.9.0b2)
1298 <!-- JAL-2085 -->Cannot save project when view has a
1299 reference sequence defined
1302 <!-- JAL-1011 -->Columns are suddenly selected in other
1303 alignments and views when revealing hidden columns
1306 <!-- JAL-1989 -->Hide columns not mirrored in complement
1307 view in a cDNA/Protein splitframe
1310 <!-- JAL-1369 -->Cannot save/restore representative
1311 sequence from project when only one sequence is
1315 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1316 in Structure Chooser
1319 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1320 structure consensus didn't refresh annotation panel
1323 <!-- JAL-1962 -->View mapping in structure view shows
1324 mappings between sequence and all chains in a PDB file
1327 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1328 dialogs format columns correctly, don't display array
1329 data, sort columns according to type
1332 <!-- JAL-1975 -->Export complete shown after destination
1333 file chooser is cancelled during an image export
1336 <!-- JAL-2025 -->Error when querying PDB Service with
1337 sequence name containing special characters
1340 <!-- JAL-2024 -->Manual PDB structure querying should be
1344 <!-- JAL-2104 -->Large tooltips with broken HTML
1345 formatting don't wrap
1348 <!-- JAL-1128 -->Figures exported from wrapped view are
1349 truncated so L looks like I in consensus annotation
1352 <!-- JAL-2003 -->Export features should only export the
1353 currently displayed features for the current selection or
1357 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1358 after fetching cross-references, and restoring from
1362 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1363 followed in the structure viewer
1366 <!-- JAL-2163 -->Titles for individual alignments in
1367 splitframe not restored from project
1370 <!-- JAL-2145 -->missing autocalculated annotation at
1371 trailing end of protein alignment in transcript/product
1372 splitview when pad-gaps not enabled by default
1375 <!-- JAL-1797 -->amino acid physicochemical conservation
1379 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1380 article has been read (reopened issue due to
1381 internationalisation problems)
1384 <!-- JAL-1960 -->Only offer PDB structures in structure
1385 viewer based on sequence name, PDB and UniProt
1390 <!-- JAL-1976 -->No progress bar shown during export of
1394 <!-- JAL-2213 -->Structures not always superimposed after
1395 multiple structures are shown for one or more sequences.
1398 <!-- JAL-1370 -->Reference sequence characters should not
1399 be replaced with '.' when 'Show unconserved' format option
1403 <!-- JAL-1823 -->Cannot specify chain code when entering
1404 specific PDB id for sequence
1407 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1408 'Export hidden sequences' is enabled, but 'export hidden
1409 columns' is disabled.
1412 <!--JAL-2026-->Best Quality option in structure chooser
1413 selects lowest rather than highest resolution structures
1417 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1418 to sequence mapping in 'View Mappings' report
1421 <!-- JAL-2284 -->Unable to read old Jalview projects that
1422 contain non-XML data added after Jalvew wrote project.
1425 <!-- JAL-2118 -->Newly created annotation row reorders
1426 after clicking on it to create new annotation for a
1429 <!-- may exclude, this is an external service stability issue JAL-1941
1430 -- > RNA 3D structure not added via DSSR service</li> -->
1435 <!-- JAL-2151 -->Incorrect columns are selected when
1436 hidden columns present before start of sequence
1439 <!-- JAL-1986 -->Missing dependencies on applet pages
1443 <!-- JAL-1947 -->Overview pixel size changes when
1444 sequences are hidden in applet
1447 <!-- JAL-1996 -->Updated instructions for applet
1448 deployment on examples pages.
1455 <td width="60" nowrap>
1456 <div align="center">
1457 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1458 <em>16/10/2015</em></strong>
1461 <td><em>General</em>
1463 <li>Time stamps for signed Jalview application and applet
1468 <em>Application</em>
1470 <li>Duplicate group consensus and conservation rows
1471 shown when tree is partitioned</li>
1472 <li>Erratic behaviour when tree partitions made with
1473 multiple cDNA/Protein split views</li>
1479 <td width="60" nowrap>
1480 <div align="center">
1481 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1482 <em>8/10/2015</em></strong>
1485 <td><em>General</em>
1487 <li>Updated Spanish translations of localized text for
1489 </ul> <em>Application</em>
1491 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1492 <li>Signed OSX InstallAnywhere installer<br></li>
1493 <li>Support for per-sequence based annotations in BioJSON</li>
1494 </ul> <em>Applet</em>
1496 <li>Split frame example added to applet examples page</li>
1497 </ul> <em>Build and Deployment</em>
1500 <!-- JAL-1888 -->New ant target for running Jalview's test
1508 <li>Mapping of cDNA to protein in split frames
1509 incorrect when sequence start > 1</li>
1510 <li>Broken images in filter column by annotation dialog
1512 <li>Feature colours not parsed from features file</li>
1513 <li>Exceptions and incomplete link URLs recovered when
1514 loading a features file containing HTML tags in feature
1518 <em>Application</em>
1520 <li>Annotations corrupted after BioJS export and
1522 <li>Incorrect sequence limits after Fetch DB References
1523 with 'trim retrieved sequences'</li>
1524 <li>Incorrect warning about deleting all data when
1525 deleting selected columns</li>
1526 <li>Patch to build system for shipping properly signed
1527 JNLP templates for webstart launch</li>
1528 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1529 unreleased structures for download or viewing</li>
1530 <li>Tab/space/return keystroke operation of EMBL-PDBe
1531 fetcher/viewer dialogs works correctly</li>
1532 <li>Disabled 'minimise' button on Jalview windows
1533 running on OSX to workaround redraw hang bug</li>
1534 <li>Split cDNA/Protein view position and geometry not
1535 recovered from jalview project</li>
1536 <li>Initial enabled/disabled state of annotation menu
1537 sorter 'show autocalculated first/last' corresponds to
1539 <li>Restoring of Clustal, RNA Helices and T-Coffee
1540 color schemes from BioJSON</li>
1544 <li>Reorder sequences mirrored in cDNA/Protein split
1546 <li>Applet with Jmol examples not loading correctly</li>
1552 <td><div align="center">
1553 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1555 <td><em>General</em>
1557 <li>Linked visualisation and analysis of DNA and Protein
1560 <li>Translated cDNA alignments shown as split protein
1561 and DNA alignment views</li>
1562 <li>Codon consensus annotation for linked protein and
1563 cDNA alignment views</li>
1564 <li>Link cDNA or Protein product sequences by loading
1565 them onto Protein or cDNA alignments</li>
1566 <li>Reconstruct linked cDNA alignment from aligned
1567 protein sequences</li>
1570 <li>Jmol integration updated to Jmol v14.2.14</li>
1571 <li>Import and export of Jalview alignment views as <a
1572 href="features/bioJsonFormat.html">BioJSON</a></li>
1573 <li>New alignment annotation file statements for
1574 reference sequences and marking hidden columns</li>
1575 <li>Reference sequence based alignment shading to
1576 highlight variation</li>
1577 <li>Select or hide columns according to alignment
1579 <li>Find option for locating sequences by description</li>
1580 <li>Conserved physicochemical properties shown in amino
1581 acid conservation row</li>
1582 <li>Alignments can be sorted by number of RNA helices</li>
1583 </ul> <em>Application</em>
1585 <li>New cDNA/Protein analysis capabilities
1587 <li>Get Cross-References should open a Split Frame
1588 view with cDNA/Protein</li>
1589 <li>Detect when nucleotide sequences and protein
1590 sequences are placed in the same alignment</li>
1591 <li>Split cDNA/Protein views are saved in Jalview
1596 <li>Use REST API to talk to Chimera</li>
1597 <li>Selected regions in Chimera are highlighted in linked
1598 Jalview windows</li>
1600 <li>VARNA RNA viewer updated to v3.93</li>
1601 <li>VARNA views are saved in Jalview Projects</li>
1602 <li>Pseudoknots displayed as Jalview RNA annotation can
1603 be shown in VARNA</li>
1605 <li>Make groups for selection uses marked columns as well
1606 as the active selected region</li>
1608 <li>Calculate UPGMA and NJ trees using sequence feature
1610 <li>New Export options
1612 <li>New Export Settings dialog to control hidden
1613 region export in flat file generation</li>
1615 <li>Export alignment views for display with the <a
1616 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1618 <li>Export scrollable SVG in HTML page</li>
1619 <li>Optional embedding of BioJSON data when exporting
1620 alignment figures to HTML</li>
1622 <li>3D structure retrieval and display
1624 <li>Free text and structured queries with the PDBe
1626 <li>PDBe Search API based discovery and selection of
1627 PDB structures for a sequence set</li>
1631 <li>JPred4 employed for protein secondary structure
1633 <li>Hide Insertions menu option to hide unaligned columns
1634 for one or a group of sequences</li>
1635 <li>Automatically hide insertions in alignments imported
1636 from the JPred4 web server</li>
1637 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1638 system on OSX<br />LGPL libraries courtesy of <a
1639 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1641 <li>changed 'View nucleotide structure' submenu to 'View
1642 VARNA 2D Structure'</li>
1643 <li>change "View protein structure" menu option to "3D
1646 </ul> <em>Applet</em>
1648 <li>New layout for applet example pages</li>
1649 <li>New parameters to enable SplitFrame view
1650 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1651 <li>New example demonstrating linked viewing of cDNA and
1652 Protein alignments</li>
1653 </ul> <em>Development and deployment</em>
1655 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1656 <li>Include installation type and git revision in build
1657 properties and console log output</li>
1658 <li>Jalview Github organisation, and new github site for
1659 storing BioJsMSA Templates</li>
1660 <li>Jalview's unit tests now managed with TestNG</li>
1663 <!-- <em>General</em>
1665 </ul> --> <!-- issues resolved --> <em>Application</em>
1667 <li>Escape should close any open find dialogs</li>
1668 <li>Typo in select-by-features status report</li>
1669 <li>Consensus RNA secondary secondary structure
1670 predictions are not highlighted in amber</li>
1671 <li>Missing gap character in v2.7 example file means
1672 alignment appears unaligned when pad-gaps is not enabled</li>
1673 <li>First switch to RNA Helices colouring doesn't colour
1674 associated structure views</li>
1675 <li>ID width preference option is greyed out when auto
1676 width checkbox not enabled</li>
1677 <li>Stopped a warning dialog from being shown when
1678 creating user defined colours</li>
1679 <li>'View Mapping' in structure viewer shows sequence
1680 mappings for just that viewer's sequences</li>
1681 <li>Workaround for superposing PDB files containing
1682 multiple models in Chimera</li>
1683 <li>Report sequence position in status bar when hovering
1684 over Jmol structure</li>
1685 <li>Cannot output gaps as '.' symbols with Selection ->
1686 output to text box</li>
1687 <li>Flat file exports of alignments with hidden columns
1688 have incorrect sequence start/end</li>
1689 <li>'Aligning' a second chain to a Chimera structure from
1691 <li>Colour schemes applied to structure viewers don't
1692 work for nucleotide</li>
1693 <li>Loading/cut'n'pasting an empty or invalid file leads
1694 to a grey/invisible alignment window</li>
1695 <li>Exported Jpred annotation from a sequence region
1696 imports to different position</li>
1697 <li>Space at beginning of sequence feature tooltips shown
1698 on some platforms</li>
1699 <li>Chimera viewer 'View | Show Chain' menu is not
1701 <li>'New View' fails with a Null Pointer Exception in
1702 console if Chimera has been opened</li>
1703 <li>Mouseover to Chimera not working</li>
1704 <li>Miscellaneous ENA XML feature qualifiers not
1706 <li>NPE in annotation renderer after 'Extract Scores'</li>
1707 <li>If two structures in one Chimera window, mouseover of
1708 either sequence shows on first structure</li>
1709 <li>'Show annotations' options should not make
1710 non-positional annotations visible</li>
1711 <li>Subsequence secondary structure annotation not shown
1712 in right place after 'view flanking regions'</li>
1713 <li>File Save As type unset when current file format is
1715 <li>Save as '.jar' option removed for saving Jalview
1717 <li>Colour by Sequence colouring in Chimera more
1719 <li>Cannot 'add reference annotation' for a sequence in
1720 several views on same alignment</li>
1721 <li>Cannot show linked products for EMBL / ENA records</li>
1722 <li>Jalview's tooltip wraps long texts containing no
1724 </ul> <em>Applet</em>
1726 <li>Jmol to JalviewLite mouseover/link not working</li>
1727 <li>JalviewLite can't import sequences with ID
1728 descriptions containing angle brackets</li>
1729 </ul> <em>General</em>
1731 <li>Cannot export and reimport RNA secondary structure
1732 via jalview annotation file</li>
1733 <li>Random helix colour palette for colour by annotation
1734 with RNA secondary structure</li>
1735 <li>Mouseover to cDNA from STOP residue in protein
1736 translation doesn't work.</li>
1737 <li>hints when using the select by annotation dialog box</li>
1738 <li>Jmol alignment incorrect if PDB file has alternate CA
1740 <li>FontChooser message dialog appears to hang after
1741 choosing 1pt font</li>
1742 <li>Peptide secondary structure incorrectly imported from
1743 annotation file when annotation display text includes 'e' or
1745 <li>Cannot set colour of new feature type whilst creating
1747 <li>cDNA translation alignment should not be sequence
1748 order dependent</li>
1749 <li>'Show unconserved' doesn't work for lower case
1751 <li>Nucleotide ambiguity codes involving R not recognised</li>
1752 </ul> <em>Deployment and Documentation</em>
1754 <li>Applet example pages appear different to the rest of
1755 www.jalview.org</li>
1756 </ul> <em>Application Known issues</em>
1758 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1759 <li>Misleading message appears after trying to delete
1761 <li>Jalview icon not shown in dock after InstallAnywhere
1762 version launches</li>
1763 <li>Fetching EMBL reference for an RNA sequence results
1764 fails with a sequence mismatch</li>
1765 <li>Corrupted or unreadable alignment display when
1766 scrolling alignment to right</li>
1767 <li>ArrayIndexOutOfBoundsException thrown when remove
1768 empty columns called on alignment with ragged gapped ends</li>
1769 <li>auto calculated alignment annotation rows do not get
1770 placed above or below non-autocalculated rows</li>
1771 <li>Jalview dekstop becomes sluggish at full screen in
1772 ultra-high resolution</li>
1773 <li>Cannot disable consensus calculation independently of
1774 quality and conservation</li>
1775 <li>Mouseover highlighting between cDNA and protein can
1776 become sluggish with more than one splitframe shown</li>
1777 </ul> <em>Applet Known Issues</em>
1779 <li>Core PDB parsing code requires Jmol</li>
1780 <li>Sequence canvas panel goes white when alignment
1781 window is being resized</li>
1787 <td><div align="center">
1788 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1790 <td><em>General</em>
1792 <li>Updated Java code signing certificate donated by
1794 <li>Features and annotation preserved when performing
1795 pairwise alignment</li>
1796 <li>RNA pseudoknot annotation can be
1797 imported/exported/displayed</li>
1798 <li>'colour by annotation' can colour by RNA and
1799 protein secondary structure</li>
1800 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1801 post-hoc with 2.9 release</em>)
1804 </ul> <em>Application</em>
1806 <li>Extract and display secondary structure for sequences
1807 with 3D structures</li>
1808 <li>Support for parsing RNAML</li>
1809 <li>Annotations menu for layout
1811 <li>sort sequence annotation rows by alignment</li>
1812 <li>place sequence annotation above/below alignment
1815 <li>Output in Stockholm format</li>
1816 <li>Internationalisation: improved Spanish (es)
1818 <li>Structure viewer preferences tab</li>
1819 <li>Disorder and Secondary Structure annotation tracks
1820 shared between alignments</li>
1821 <li>UCSF Chimera launch and linked highlighting from
1823 <li>Show/hide all sequence associated annotation rows for
1824 all or current selection</li>
1825 <li>disorder and secondary structure predictions
1826 available as dataset annotation</li>
1827 <li>Per-sequence rna helices colouring</li>
1830 <li>Sequence database accessions imported when fetching
1831 alignments from Rfam</li>
1832 <li>update VARNA version to 3.91</li>
1834 <li>New groovy scripts for exporting aligned positions,
1835 conservation values, and calculating sum of pairs scores.</li>
1836 <li>Command line argument to set default JABAWS server</li>
1837 <li>include installation type in build properties and
1838 console log output</li>
1839 <li>Updated Jalview project format to preserve dataset
1843 <!-- issues resolved --> <em>Application</em>
1845 <li>Distinguish alignment and sequence associated RNA
1846 structure in structure->view->VARNA</li>
1847 <li>Raise dialog box if user deletes all sequences in an
1849 <li>Pressing F1 results in documentation opening twice</li>
1850 <li>Sequence feature tooltip is wrapped</li>
1851 <li>Double click on sequence associated annotation
1852 selects only first column</li>
1853 <li>Redundancy removal doesn't result in unlinked
1854 leaves shown in tree</li>
1855 <li>Undos after several redundancy removals don't undo
1857 <li>Hide sequence doesn't hide associated annotation</li>
1858 <li>User defined colours dialog box too big to fit on
1859 screen and buttons not visible</li>
1860 <li>author list isn't updated if already written to
1861 Jalview properties</li>
1862 <li>Popup menu won't open after retrieving sequence
1864 <li>File open window for associate PDB doesn't open</li>
1865 <li>Left-then-right click on a sequence id opens a
1866 browser search window</li>
1867 <li>Cannot open sequence feature shading/sort popup menu
1868 in feature settings dialog</li>
1869 <li>better tooltip placement for some areas of Jalview
1871 <li>Allow addition of JABAWS Server which doesn't
1872 pass validation</li>
1873 <li>Web services parameters dialog box is too large to
1875 <li>Muscle nucleotide alignment preset obscured by
1877 <li>JABAWS preset submenus don't contain newly
1878 defined user preset</li>
1879 <li>MSA web services warns user if they were launched
1880 with invalid input</li>
1881 <li>Jalview cannot contact DAS Registy when running on
1884 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1885 'Superpose with' submenu not shown when new view
1889 </ul> <!-- <em>Applet</em>
1891 </ul> <em>General</em>
1893 </ul>--> <em>Deployment and Documentation</em>
1895 <li>2G and 1G options in launchApp have no effect on
1896 memory allocation</li>
1897 <li>launchApp service doesn't automatically open
1898 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1900 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1901 InstallAnywhere reports cannot find valid JVM when Java
1902 1.7_055 is available
1904 </ul> <em>Application Known issues</em>
1907 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1908 corrupted or unreadable alignment display when scrolling
1912 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1913 retrieval fails but progress bar continues for DAS retrieval
1914 with large number of ID
1917 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1918 flatfile output of visible region has incorrect sequence
1922 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1923 rna structure consensus doesn't update when secondary
1924 structure tracks are rearranged
1927 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1928 invalid rna structure positional highlighting does not
1929 highlight position of invalid base pairs
1932 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1933 out of memory errors are not raised when saving Jalview
1934 project from alignment window file menu
1937 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1938 Switching to RNA Helices colouring doesn't propagate to
1942 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1943 colour by RNA Helices not enabled when user created
1944 annotation added to alignment
1947 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1948 Jalview icon not shown on dock in Mountain Lion/Webstart
1950 </ul> <em>Applet Known Issues</em>
1953 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1954 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1957 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1958 Jalview and Jmol example not compatible with IE9
1961 <li>Sort by annotation score doesn't reverse order
1967 <td><div align="center">
1968 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1971 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1974 <li>Internationalisation of user interface (usually
1975 called i18n support) and translation for Spanish locale</li>
1976 <li>Define/Undefine group on current selection with
1977 Ctrl-G/Shift Ctrl-G</li>
1978 <li>Improved group creation/removal options in
1979 alignment/sequence Popup menu</li>
1980 <li>Sensible precision for symbol distribution
1981 percentages shown in logo tooltip.</li>
1982 <li>Annotation panel height set according to amount of
1983 annotation when alignment first opened</li>
1984 </ul> <em>Application</em>
1986 <li>Interactive consensus RNA secondary structure
1987 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1988 <li>Select columns containing particular features from
1989 Feature Settings dialog</li>
1990 <li>View all 'representative' PDB structures for selected
1992 <li>Update Jalview project format:
1994 <li>New file extension for Jalview projects '.jvp'</li>
1995 <li>Preserve sequence and annotation dataset (to
1996 store secondary structure annotation,etc)</li>
1997 <li>Per group and alignment annotation and RNA helix
2001 <li>New similarity measures for PCA and Tree calculation
2003 <li>Experimental support for retrieval and viewing of
2004 flanking regions for an alignment</li>
2008 <!-- issues resolved --> <em>Application</em>
2010 <li>logo keeps spinning and status remains at queued or
2011 running after job is cancelled</li>
2012 <li>cannot export features from alignments imported from
2013 Jalview/VAMSAS projects</li>
2014 <li>Buggy slider for web service parameters that take
2016 <li>Newly created RNA secondary structure line doesn't
2017 have 'display all symbols' flag set</li>
2018 <li>T-COFFEE alignment score shading scheme and other
2019 annotation shading not saved in Jalview project</li>
2020 <li>Local file cannot be loaded in freshly downloaded
2022 <li>Jalview icon not shown on dock in Mountain
2024 <li>Load file from desktop file browser fails</li>
2025 <li>Occasional NPE thrown when calculating large trees</li>
2026 <li>Cannot reorder or slide sequences after dragging an
2027 alignment onto desktop</li>
2028 <li>Colour by annotation dialog throws NPE after using
2029 'extract scores' function</li>
2030 <li>Loading/cut'n'pasting an empty file leads to a grey
2031 alignment window</li>
2032 <li>Disorder thresholds rendered incorrectly after
2033 performing IUPred disorder prediction</li>
2034 <li>Multiple group annotated consensus rows shown when
2035 changing 'normalise logo' display setting</li>
2036 <li>Find shows blank dialog after 'finished searching' if
2037 nothing matches query</li>
2038 <li>Null Pointer Exceptions raised when sorting by
2039 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
2041 <li>Errors in Jmol console when structures in alignment
2042 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
2044 <li>Not all working JABAWS services are shown in
2046 <li>JAVAWS version of Jalview fails to launch with
2047 'invalid literal/length code'</li>
2048 <li>Annotation/RNA Helix colourschemes cannot be applied
2049 to alignment with groups (actually fixed in 2.8.0b1)</li>
2050 <li>RNA Helices and T-Coffee Scores available as default
2053 </ul> <em>Applet</em>
2055 <li>Remove group option is shown even when selection is
2057 <li>Apply to all groups ticked but colourscheme changes
2058 don't affect groups</li>
2059 <li>Documented RNA Helices and T-Coffee Scores as valid
2060 colourscheme name</li>
2061 <li>Annotation labels drawn on sequence IDs when
2062 Annotation panel is not displayed</li>
2063 <li>Increased font size for dropdown menus on OSX and
2064 embedded windows</li>
2065 </ul> <em>Other</em>
2067 <li>Consensus sequence for alignments/groups with a
2068 single sequence were not calculated</li>
2069 <li>annotation files that contain only groups imported as
2070 annotation and junk sequences</li>
2071 <li>Fasta files with sequences containing '*' incorrectly
2072 recognised as PFAM or BLC</li>
2073 <li>conservation/PID slider apply all groups option
2074 doesn't affect background (2.8.0b1)
2076 <li>redundancy highlighting is erratic at 0% and 100%</li>
2077 <li>Remove gapped columns fails for sequences with ragged
2079 <li>AMSA annotation row with leading spaces is not
2080 registered correctly on import</li>
2081 <li>Jalview crashes when selecting PCA analysis for
2082 certain alignments</li>
2083 <li>Opening the colour by annotation dialog for an
2084 existing annotation based 'use original colours'
2085 colourscheme loses original colours setting</li>
2090 <td><div align="center">
2091 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2092 <em>30/1/2014</em></strong>
2096 <li>Trusted certificates for JalviewLite applet and
2097 Jalview Desktop application<br />Certificate was donated by
2098 <a href="https://www.certum.eu">Certum</a> to the Jalview
2099 open source project).
2101 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2102 <li>Output in Stockholm format</li>
2103 <li>Allow import of data from gzipped files</li>
2104 <li>Export/import group and sequence associated line
2105 graph thresholds</li>
2106 <li>Nucleotide substitution matrix that supports RNA and
2107 ambiguity codes</li>
2108 <li>Allow disorder predictions to be made on the current
2109 selection (or visible selection) in the same way that JPred
2111 <li>Groovy scripting for headless Jalview operation</li>
2112 </ul> <em>Other improvements</em>
2114 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2115 <li>COMBINE statement uses current SEQUENCE_REF and
2116 GROUP_REF scope to group annotation rows</li>
2117 <li>Support '' style escaping of quotes in Newick
2119 <li>Group options for JABAWS service by command line name</li>
2120 <li>Empty tooltip shown for JABA service options with a
2121 link but no description</li>
2122 <li>Select primary source when selecting authority in
2123 database fetcher GUI</li>
2124 <li>Add .mfa to FASTA file extensions recognised by
2126 <li>Annotation label tooltip text wrap</li>
2131 <li>Slow scrolling when lots of annotation rows are
2133 <li>Lots of NPE (and slowness) after creating RNA
2134 secondary structure annotation line</li>
2135 <li>Sequence database accessions not imported when
2136 fetching alignments from Rfam</li>
2137 <li>Incorrect SHMR submission for sequences with
2139 <li>View all structures does not always superpose
2141 <li>Option widgets in service parameters not updated to
2142 reflect user or preset settings</li>
2143 <li>Null pointer exceptions for some services without
2144 presets or adjustable parameters</li>
2145 <li>Discover PDB IDs entry in structure menu doesn't
2146 discover PDB xRefs</li>
2147 <li>Exception encountered while trying to retrieve
2148 features with DAS</li>
2149 <li>Lowest value in annotation row isn't coloured
2150 when colour by annotation (per sequence) is coloured</li>
2151 <li>Keyboard mode P jumps to start of gapped region when
2152 residue follows a gap</li>
2153 <li>Jalview appears to hang importing an alignment with
2154 Wrap as default or after enabling Wrap</li>
2155 <li>'Right click to add annotations' message
2156 shown in wrap mode when no annotations present</li>
2157 <li>Disorder predictions fail with NPE if no automatic
2158 annotation already exists on alignment</li>
2159 <li>oninit javascript function should be called after
2160 initialisation completes</li>
2161 <li>Remove redundancy after disorder prediction corrupts
2162 alignment window display</li>
2163 <li>Example annotation file in documentation is invalid</li>
2164 <li>Grouped line graph annotation rows are not exported
2165 to annotation file</li>
2166 <li>Multi-harmony analysis cannot be run when only two
2168 <li>Cannot create multiple groups of line graphs with
2169 several 'combine' statements in annotation file</li>
2170 <li>Pressing return several times causes Number Format
2171 exceptions in keyboard mode</li>
2172 <li>Multi-harmony (SHMMR) method doesn't submit
2173 correct partitions for input data</li>
2174 <li>Translation from DNA to Amino Acids fails</li>
2175 <li>Jalview fail to load newick tree with quoted label</li>
2176 <li>--headless flag isn't understood</li>
2177 <li>ClassCastException when generating EPS in headless
2179 <li>Adjusting sequence-associated shading threshold only
2180 changes one row's threshold</li>
2181 <li>Preferences and Feature settings panel panel
2182 doesn't open</li>
2183 <li>hide consensus histogram also hides conservation and
2184 quality histograms</li>
2189 <td><div align="center">
2190 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2192 <td><em>Application</em>
2194 <li>Support for JABAWS 2.0 Services (AACon alignment
2195 conservation, protein disorder and Clustal Omega)</li>
2196 <li>JABAWS server status indicator in Web Services
2198 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2199 in Jalview alignment window</li>
2200 <li>Updated Jalview build and deploy framework for OSX
2201 mountain lion, windows 7, and 8</li>
2202 <li>Nucleotide substitution matrix for PCA that supports
2203 RNA and ambiguity codes</li>
2205 <li>Improved sequence database retrieval GUI</li>
2206 <li>Support fetching and database reference look up
2207 against multiple DAS sources (Fetch all from in 'fetch db
2209 <li>Jalview project improvements
2211 <li>Store and retrieve the 'belowAlignment'
2212 flag for annotation</li>
2213 <li>calcId attribute to group annotation rows on the
2215 <li>Store AACon calculation settings for a view in
2216 Jalview project</li>
2220 <li>horizontal scrolling gesture support</li>
2221 <li>Visual progress indicator when PCA calculation is
2223 <li>Simpler JABA web services menus</li>
2224 <li>visual indication that web service results are still
2225 being retrieved from server</li>
2226 <li>Serialise the dialogs that are shown when Jalview
2227 starts up for first time</li>
2228 <li>Jalview user agent string for interacting with HTTP
2230 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2232 <li>Examples directory and Groovy library included in
2233 InstallAnywhere distribution</li>
2234 </ul> <em>Applet</em>
2236 <li>RNA alignment and secondary structure annotation
2237 visualization applet example</li>
2238 </ul> <em>General</em>
2240 <li>Normalise option for consensus sequence logo</li>
2241 <li>Reset button in PCA window to return dimensions to
2243 <li>Allow seqspace or Jalview variant of alignment PCA
2245 <li>PCA with either nucleic acid and protein substitution
2247 <li>Allow windows containing HTML reports to be exported
2249 <li>Interactive display and editing of RNA secondary
2250 structure contacts</li>
2251 <li>RNA Helix Alignment Colouring</li>
2252 <li>RNA base pair logo consensus</li>
2253 <li>Parse sequence associated secondary structure
2254 information in Stockholm files</li>
2255 <li>HTML Export database accessions and annotation
2256 information presented in tooltip for sequences</li>
2257 <li>Import secondary structure from LOCARNA clustalw
2258 style RNA alignment files</li>
2259 <li>import and visualise T-COFFEE quality scores for an
2261 <li>'colour by annotation' per sequence option to
2262 shade each sequence according to its associated alignment
2264 <li>New Jalview Logo</li>
2265 </ul> <em>Documentation and Development</em>
2267 <li>documentation for score matrices used in Jalview</li>
2268 <li>New Website!</li>
2270 <td><em>Application</em>
2272 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2273 wsdbfetch REST service</li>
2274 <li>Stop windows being moved outside desktop on OSX</li>
2275 <li>Filetype associations not installed for webstart
2277 <li>Jalview does not always retrieve progress of a JABAWS
2278 job execution in full once it is complete</li>
2279 <li>revise SHMR RSBS definition to ensure alignment is
2280 uploaded via ali_file parameter</li>
2281 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2282 <li>View all structures superposed fails with exception</li>
2283 <li>Jnet job queues forever if a very short sequence is
2284 submitted for prediction</li>
2285 <li>Cut and paste menu not opened when mouse clicked on
2287 <li>Putting fractional value into integer text box in
2288 alignment parameter dialog causes Jalview to hang</li>
2289 <li>Structure view highlighting doesn't work on
2291 <li>View all structures fails with exception shown in
2293 <li>Characters in filename associated with PDBEntry not
2294 escaped in a platform independent way</li>
2295 <li>Jalview desktop fails to launch with exception when
2297 <li>Tree calculation reports 'you must have 2 or more
2298 sequences selected' when selection is empty</li>
2299 <li>Jalview desktop fails to launch with jar signature
2300 failure when java web start temporary file caching is
2302 <li>DAS Sequence retrieval with range qualification
2303 results in sequence xref which includes range qualification</li>
2304 <li>Errors during processing of command line arguments
2305 cause progress bar (JAL-898) to be removed</li>
2306 <li>Replace comma for semi-colon option not disabled for
2307 DAS sources in sequence fetcher</li>
2308 <li>Cannot close news reader when JABAWS server warning
2309 dialog is shown</li>
2310 <li>Option widgets not updated to reflect user settings</li>
2311 <li>Edited sequence not submitted to web service</li>
2312 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2313 <li>InstallAnywhere installer doesn't unpack and run
2314 on OSX Mountain Lion</li>
2315 <li>Annotation panel not given a scroll bar when
2316 sequences with alignment annotation are pasted into the
2318 <li>Sequence associated annotation rows not associated
2319 when loaded from Jalview project</li>
2320 <li>Browser launch fails with NPE on java 1.7</li>
2321 <li>JABAWS alignment marked as finished when job was
2322 cancelled or job failed due to invalid input</li>
2323 <li>NPE with v2.7 example when clicking on Tree
2324 associated with all views</li>
2325 <li>Exceptions when copy/paste sequences with grouped
2326 annotation rows to new window</li>
2327 </ul> <em>Applet</em>
2329 <li>Sequence features are momentarily displayed before
2330 they are hidden using hidefeaturegroups applet parameter</li>
2331 <li>loading features via javascript API automatically
2332 enables feature display</li>
2333 <li>scrollToColumnIn javascript API method doesn't
2335 </ul> <em>General</em>
2337 <li>Redundancy removal fails for rna alignment</li>
2338 <li>PCA calculation fails when sequence has been selected
2339 and then deselected</li>
2340 <li>PCA window shows grey box when first opened on OSX</li>
2341 <li>Letters coloured pink in sequence logo when alignment
2342 coloured with clustalx</li>
2343 <li>Choosing fonts without letter symbols defined causes
2344 exceptions and redraw errors</li>
2345 <li>Initial PCA plot view is not same as manually
2346 reconfigured view</li>
2347 <li>Grouped annotation graph label has incorrect line
2349 <li>Grouped annotation graph label display is corrupted
2350 for lots of labels</li>
2355 <div align="center">
2356 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2359 <td><em>Application</em>
2361 <li>Jalview Desktop News Reader</li>
2362 <li>Tweaked default layout of web services menu</li>
2363 <li>View/alignment association menu to enable user to
2364 easily specify which alignment a multi-structure view takes
2365 its colours/correspondences from</li>
2366 <li>Allow properties file location to be specified as URL</li>
2367 <li>Extend Jalview project to preserve associations
2368 between many alignment views and a single Jmol display</li>
2369 <li>Store annotation row height in Jalview project file</li>
2370 <li>Annotation row column label formatting attributes
2371 stored in project file</li>
2372 <li>Annotation row order for auto-calculated annotation
2373 rows preserved in Jalview project file</li>
2374 <li>Visual progress indication when Jalview state is
2375 saved using Desktop window menu</li>
2376 <li>Visual indication that command line arguments are
2377 still being processed</li>
2378 <li>Groovy script execution from URL</li>
2379 <li>Colour by annotation default min and max colours in
2381 <li>Automatically associate PDB files dragged onto an
2382 alignment with sequences that have high similarity and
2384 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2385 <li>'view structures' option to open many
2386 structures in same window</li>
2387 <li>Sort associated views menu option for tree panel</li>
2388 <li>Group all JABA and non-JABA services for a particular
2389 analysis function in its own submenu</li>
2390 </ul> <em>Applet</em>
2392 <li>Userdefined and autogenerated annotation rows for
2394 <li>Adjustment of alignment annotation pane height</li>
2395 <li>Annotation scrollbar for annotation panel</li>
2396 <li>Drag to reorder annotation rows in annotation panel</li>
2397 <li>'automaticScrolling' parameter</li>
2398 <li>Allow sequences with partial ID string matches to be
2399 annotated from GFF/Jalview features files</li>
2400 <li>Sequence logo annotation row in applet</li>
2401 <li>Absolute paths relative to host server in applet
2402 parameters are treated as such</li>
2403 <li>New in the JalviewLite javascript API:
2405 <li>JalviewLite.js javascript library</li>
2406 <li>Javascript callbacks for
2408 <li>Applet initialisation</li>
2409 <li>Sequence/alignment mouse-overs and selections</li>
2412 <li>scrollTo row and column alignment scrolling
2414 <li>Select sequence/alignment regions from javascript</li>
2415 <li>javascript structure viewer harness to pass
2416 messages between Jmol and Jalview when running as
2417 distinct applets</li>
2418 <li>sortBy method</li>
2419 <li>Set of applet and application examples shipped
2420 with documentation</li>
2421 <li>New example to demonstrate JalviewLite and Jmol
2422 javascript message exchange</li>
2424 </ul> <em>General</em>
2426 <li>Enable Jmol displays to be associated with multiple
2427 multiple alignments</li>
2428 <li>Option to automatically sort alignment with new tree</li>
2429 <li>User configurable link to enable redirects to a
2430 www.Jalview.org mirror</li>
2431 <li>Jmol colours option for Jmol displays</li>
2432 <li>Configurable newline string when writing alignment
2433 and other flat files</li>
2434 <li>Allow alignment annotation description lines to
2435 contain html tags</li>
2436 </ul> <em>Documentation and Development</em>
2438 <li>Add groovy test harness for bulk load testing to
2440 <li>Groovy script to load and align a set of sequences
2441 using a web service before displaying the result in the
2442 Jalview desktop</li>
2443 <li>Restructured javascript and applet api documentation</li>
2444 <li>Ant target to publish example html files with applet
2446 <li>Netbeans project for building Jalview from source</li>
2447 <li>ant task to create online javadoc for Jalview source</li>
2449 <td><em>Application</em>
2451 <li>User defined colourscheme throws exception when
2452 current built in colourscheme is saved as new scheme</li>
2453 <li>AlignFrame->Save in application pops up save
2454 dialog for valid filename/format</li>
2455 <li>Cannot view associated structure for UniProt sequence</li>
2456 <li>PDB file association breaks for UniProt sequence
2458 <li>Associate PDB from file dialog does not tell you
2459 which sequence is to be associated with the file</li>
2460 <li>Find All raises null pointer exception when query
2461 only matches sequence IDs</li>
2462 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2463 <li>Jalview project with Jmol views created with Jalview
2464 2.4 cannot be loaded</li>
2465 <li>Filetype associations not installed for webstart
2467 <li>Two or more chains in a single PDB file associated
2468 with sequences in different alignments do not get coloured
2469 by their associated sequence</li>
2470 <li>Visibility status of autocalculated annotation row
2471 not preserved when project is loaded</li>
2472 <li>Annotation row height and visibility attributes not
2473 stored in Jalview project</li>
2474 <li>Tree bootstraps are not preserved when saved as a
2475 Jalview project</li>
2476 <li>Envision2 workflow tooltips are corrupted</li>
2477 <li>Enabling show group conservation also enables colour
2478 by conservation</li>
2479 <li>Duplicate group associated conservation or consensus
2480 created on new view</li>
2481 <li>Annotation scrollbar not displayed after 'show
2482 all hidden annotation rows' option selected</li>
2483 <li>Alignment quality not updated after alignment
2484 annotation row is hidden then shown</li>
2485 <li>Preserve colouring of structures coloured by
2486 sequences in pre Jalview 2.7 projects</li>
2487 <li>Web service job parameter dialog is not laid out
2489 <li>Web services menu not refreshed after 'reset
2490 services' button is pressed in preferences</li>
2491 <li>Annotation off by one in Jalview v2_3 example project</li>
2492 <li>Structures imported from file and saved in project
2493 get name like jalview_pdb1234.txt when reloaded</li>
2494 <li>Jalview does not always retrieve progress of a JABAWS
2495 job execution in full once it is complete</li>
2496 </ul> <em>Applet</em>
2498 <li>Alignment height set incorrectly when lots of
2499 annotation rows are displayed</li>
2500 <li>Relative URLs in feature HTML text not resolved to
2502 <li>View follows highlighting does not work for positions
2504 <li><= shown as = in tooltip</li>
2505 <li>Export features raises exception when no features
2507 <li>Separator string used for serialising lists of IDs
2508 for javascript api is modified when separator string
2509 provided as parameter</li>
2510 <li>Null pointer exception when selecting tree leaves for
2511 alignment with no existing selection</li>
2512 <li>Relative URLs for datasources assumed to be relative
2513 to applet's codebase</li>
2514 <li>Status bar not updated after finished searching and
2515 search wraps around to first result</li>
2516 <li>StructureSelectionManager instance shared between
2517 several Jalview applets causes race conditions and memory
2519 <li>Hover tooltip and mouseover of position on structure
2520 not sent from Jmol in applet</li>
2521 <li>Certain sequences of javascript method calls to
2522 applet API fatally hang browser</li>
2523 </ul> <em>General</em>
2525 <li>View follows structure mouseover scrolls beyond
2526 position with wrapped view and hidden regions</li>
2527 <li>Find sequence position moves to wrong residue
2528 with/without hidden columns</li>
2529 <li>Sequence length given in alignment properties window
2531 <li>InvalidNumberFormat exceptions thrown when trying to
2532 import PDB like structure files</li>
2533 <li>Positional search results are only highlighted
2534 between user-supplied sequence start/end bounds</li>
2535 <li>End attribute of sequence is not validated</li>
2536 <li>Find dialog only finds first sequence containing a
2537 given sequence position</li>
2538 <li>Sequence numbering not preserved in MSF alignment
2540 <li>Jalview PDB file reader does not extract sequence
2541 from nucleotide chains correctly</li>
2542 <li>Structure colours not updated when tree partition
2543 changed in alignment</li>
2544 <li>Sequence associated secondary structure not correctly
2545 parsed in interleaved stockholm</li>
2546 <li>Colour by annotation dialog does not restore current
2548 <li>Hiding (nearly) all sequences doesn't work
2550 <li>Sequences containing lowercase letters are not
2551 properly associated with their pdb files</li>
2552 </ul> <em>Documentation and Development</em>
2554 <li>schemas/JalviewWsParamSet.xsd corrupted by
2555 ApplyCopyright tool</li>
2560 <div align="center">
2561 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2564 <td><em>Application</em>
2566 <li>New warning dialog when the Jalview Desktop cannot
2567 contact web services</li>
2568 <li>JABA service parameters for a preset are shown in
2569 service job window</li>
2570 <li>JABA Service menu entries reworded</li>
2574 <li>Modeller PIR IO broken - cannot correctly import a
2575 pir file emitted by Jalview</li>
2576 <li>Existing feature settings transferred to new
2577 alignment view created from cut'n'paste</li>
2578 <li>Improved test for mixed amino/nucleotide chains when
2579 parsing PDB files</li>
2580 <li>Consensus and conservation annotation rows
2581 occasionally become blank for all new windows</li>
2582 <li>Exception raised when right clicking above sequences
2583 in wrapped view mode</li>
2584 </ul> <em>Application</em>
2586 <li>multiple multiply aligned structure views cause cpu
2587 usage to hit 100% and computer to hang</li>
2588 <li>Web Service parameter layout breaks for long user
2589 parameter names</li>
2590 <li>Jaba service discovery hangs desktop if Jaba server
2597 <div align="center">
2598 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2601 <td><em>Application</em>
2603 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2604 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2607 <li>Web Services preference tab</li>
2608 <li>Analysis parameters dialog box and user defined
2610 <li>Improved speed and layout of Envision2 service menu</li>
2611 <li>Superpose structures using associated sequence
2613 <li>Export coordinates and projection as CSV from PCA
2615 </ul> <em>Applet</em>
2617 <li>enable javascript: execution by the applet via the
2618 link out mechanism</li>
2619 </ul> <em>Other</em>
2621 <li>Updated the Jmol Jalview interface to work with Jmol
2623 <li>The Jalview Desktop and JalviewLite applet now
2624 require Java 1.5</li>
2625 <li>Allow Jalview feature colour specification for GFF
2626 sequence annotation files</li>
2627 <li>New 'colour by label' keword in Jalview feature file
2628 type colour specification</li>
2629 <li>New Jalview Desktop Groovy API method that allows a
2630 script to check if it being run in an interactive session or
2631 in a batch operation from the Jalview command line</li>
2635 <li>clustalx colourscheme colours Ds preferentially when
2636 both D+E are present in over 50% of the column</li>
2637 </ul> <em>Application</em>
2639 <li>typo in AlignmentFrame->View->Hide->all but
2640 selected Regions menu item</li>
2641 <li>sequence fetcher replaces ',' for ';' when the ',' is
2642 part of a valid accession ID</li>
2643 <li>fatal OOM if object retrieved by sequence fetcher
2644 runs out of memory</li>
2645 <li>unhandled Out of Memory Error when viewing pca
2646 analysis results</li>
2647 <li>InstallAnywhere builds fail to launch on OS X java
2648 10.5 update 4 (due to apple Java 1.6 update)</li>
2649 <li>Installanywhere Jalview silently fails to launch</li>
2650 </ul> <em>Applet</em>
2652 <li>Jalview.getFeatureGroups() raises an
2653 ArrayIndexOutOfBoundsException if no feature groups are
2660 <div align="center">
2661 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2667 <li>Alignment prettyprinter doesn't cope with long
2669 <li>clustalx colourscheme colours Ds preferentially when
2670 both D+E are present in over 50% of the column</li>
2671 <li>nucleic acid structures retrieved from PDB do not
2672 import correctly</li>
2673 <li>More columns get selected than were clicked on when a
2674 number of columns are hidden</li>
2675 <li>annotation label popup menu not providing correct
2676 add/hide/show options when rows are hidden or none are
2678 <li>Stockholm format shown in list of readable formats,
2679 and parser copes better with alignments from RFAM.</li>
2680 <li>CSV output of consensus only includes the percentage
2681 of all symbols if sequence logo display is enabled</li>
2683 </ul> <em>Applet</em>
2685 <li>annotation panel disappears when annotation is
2687 </ul> <em>Application</em>
2689 <li>Alignment view not redrawn properly when new
2690 alignment opened where annotation panel is visible but no
2691 annotations are present on alignment</li>
2692 <li>pasted region containing hidden columns is
2693 incorrectly displayed in new alignment window</li>
2694 <li>Jalview slow to complete operations when stdout is
2695 flooded (fix is to close the Jalview console)</li>
2696 <li>typo in AlignmentFrame->View->Hide->all but
2697 selected Rregions menu item.</li>
2698 <li>inconsistent group submenu and Format submenu entry
2699 'Un' or 'Non'conserved</li>
2700 <li>Sequence feature settings are being shared by
2701 multiple distinct alignments</li>
2702 <li>group annotation not recreated when tree partition is
2704 <li>double click on group annotation to select sequences
2705 does not propagate to associated trees</li>
2706 <li>Mac OSX specific issues:
2708 <li>exception raised when mouse clicked on desktop
2709 window background</li>
2710 <li>Desktop menu placed on menu bar and application
2711 name set correctly</li>
2712 <li>sequence feature settings not wide enough for the
2713 save feature colourscheme button</li>
2722 <div align="center">
2723 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2726 <td><em>New Capabilities</em>
2728 <li>URL links generated from description line for
2729 regular-expression based URL links (applet and application)
2731 <li>Non-positional feature URL links are shown in link
2733 <li>Linked viewing of nucleic acid sequences and
2735 <li>Automatic Scrolling option in View menu to display
2736 the currently highlighted region of an alignment.</li>
2737 <li>Order an alignment by sequence length, or using the
2738 average score or total feature count for each sequence.</li>
2739 <li>Shading features by score or associated description</li>
2740 <li>Subdivide alignment and groups based on identity of
2741 selected subsequence (Make Groups from Selection).</li>
2742 <li>New hide/show options including Shift+Control+H to
2743 hide everything but the currently selected region.</li>
2744 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2745 </ul> <em>Application</em>
2747 <li>Fetch DB References capabilities and UI expanded to
2748 support retrieval from DAS sequence sources</li>
2749 <li>Local DAS Sequence sources can be added via the
2750 command line or via the Add local source dialog box.</li>
2751 <li>DAS Dbref and DbxRef feature types are parsed as
2752 database references and protein_name is parsed as
2753 description line (BioSapiens terms).</li>
2754 <li>Enable or disable non-positional feature and database
2755 references in sequence ID tooltip from View menu in
2757 <!-- <li>New hidden columns and rows and representatives capabilities
2758 in annotations file (in progress - not yet fully implemented)</li> -->
2759 <li>Group-associated consensus, sequence logos and
2760 conservation plots</li>
2761 <li>Symbol distributions for each column can be exported
2762 and visualized as sequence logos</li>
2763 <li>Optionally scale multi-character column labels to fit
2764 within each column of annotation row<!-- todo for applet -->
2766 <li>Optional automatic sort of associated alignment view
2767 when a new tree is opened.</li>
2768 <li>Jalview Java Console</li>
2769 <li>Better placement of desktop window when moving
2770 between different screens.</li>
2771 <li>New preference items for sequence ID tooltip and
2772 consensus annotation</li>
2773 <li>Client to submit sequences and IDs to Envision2
2775 <li><em>Vamsas Capabilities</em>
2777 <li>Improved VAMSAS synchronization (Jalview archive
2778 used to preserve views, structures, and tree display
2780 <li>Import of vamsas documents from disk or URL via
2782 <li>Sharing of selected regions between views and
2783 with other VAMSAS applications (Experimental feature!)</li>
2784 <li>Updated API to VAMSAS version 0.2</li>
2786 </ul> <em>Applet</em>
2788 <li>Middle button resizes annotation row height</li>
2791 <li>sortByTree (true/false) - automatically sort the
2792 associated alignment view by the tree when a new tree is
2794 <li>showTreeBootstraps (true/false) - show or hide
2795 branch bootstraps (default is to show them if available)</li>
2796 <li>showTreeDistances (true/false) - show or hide
2797 branch lengths (default is to show them if available)</li>
2798 <li>showUnlinkedTreeNodes (true/false) - indicate if
2799 unassociated nodes should be highlighted in the tree
2801 <li>heightScale and widthScale (1.0 or more) -
2802 increase the height or width of a cell in the alignment
2803 grid relative to the current font size.</li>
2806 <li>Non-positional features displayed in sequence ID
2808 </ul> <em>Other</em>
2810 <li>Features format: graduated colour definitions and
2811 specification of feature scores</li>
2812 <li>Alignment Annotations format: new keywords for group
2813 associated annotation (GROUP_REF) and annotation row display
2814 properties (ROW_PROPERTIES)</li>
2815 <li>XML formats extended to support graduated feature
2816 colourschemes, group associated annotation, and profile
2817 visualization settings.</li></td>
2820 <li>Source field in GFF files parsed as feature source
2821 rather than description</li>
2822 <li>Non-positional features are now included in sequence
2823 feature and gff files (controlled via non-positional feature
2824 visibility in tooltip).</li>
2825 <li>URL links generated for all feature links (bugfix)</li>
2826 <li>Added URL embedding instructions to features file
2828 <li>Codons containing ambiguous nucleotides translated as
2829 'X' in peptide product</li>
2830 <li>Match case switch in find dialog box works for both
2831 sequence ID and sequence string and query strings do not
2832 have to be in upper case to match case-insensitively.</li>
2833 <li>AMSA files only contain first column of
2834 multi-character column annotation labels</li>
2835 <li>Jalview Annotation File generation/parsing consistent
2836 with documentation (e.g. Stockholm annotation can be
2837 exported and re-imported)</li>
2838 <li>PDB files without embedded PDB IDs given a friendly
2840 <li>Find incrementally searches ID string matches as well
2841 as subsequence matches, and correctly reports total number
2845 <li>Better handling of exceptions during sequence
2847 <li>Dasobert generated non-positional feature URL
2848 link text excludes the start_end suffix</li>
2849 <li>DAS feature and source retrieval buttons disabled
2850 when fetch or registry operations in progress.</li>
2851 <li>PDB files retrieved from URLs are cached properly</li>
2852 <li>Sequence description lines properly shared via
2854 <li>Sequence fetcher fetches multiple records for all
2856 <li>Ensured that command line das feature retrieval
2857 completes before alignment figures are generated.</li>
2858 <li>Reduced time taken when opening file browser for
2860 <li>isAligned check prior to calculating tree, PCA or
2861 submitting an MSA to JNet now excludes hidden sequences.</li>
2862 <li>User defined group colours properly recovered
2863 from Jalview projects.</li>
2872 <div align="center">
2873 <strong>2.4.0.b2</strong><br> 28/10/2009
2878 <li>Experimental support for google analytics usage
2880 <li>Jalview privacy settings (user preferences and docs).</li>
2885 <li>Race condition in applet preventing startup in
2887 <li>Exception when feature created from selection beyond
2888 length of sequence.</li>
2889 <li>Allow synthetic PDB files to be imported gracefully</li>
2890 <li>Sequence associated annotation rows associate with
2891 all sequences with a given id</li>
2892 <li>Find function matches case-insensitively for sequence
2893 ID string searches</li>
2894 <li>Non-standard characters do not cause pairwise
2895 alignment to fail with exception</li>
2896 </ul> <em>Application Issues</em>
2898 <li>Sequences are now validated against EMBL database</li>
2899 <li>Sequence fetcher fetches multiple records for all
2901 </ul> <em>InstallAnywhere Issues</em>
2903 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2904 issue with installAnywhere mechanism)</li>
2905 <li>Command line launching of JARs from InstallAnywhere
2906 version (java class versioning error fixed)</li>
2913 <div align="center">
2914 <strong>2.4</strong><br> 27/8/2008
2917 <td><em>User Interface</em>
2919 <li>Linked highlighting of codon and amino acid from
2920 translation and protein products</li>
2921 <li>Linked highlighting of structure associated with
2922 residue mapping to codon position</li>
2923 <li>Sequence Fetcher provides example accession numbers
2924 and 'clear' button</li>
2925 <li>MemoryMonitor added as an option under Desktop's
2927 <li>Extract score function to parse whitespace separated
2928 numeric data in description line</li>
2929 <li>Column labels in alignment annotation can be centred.</li>
2930 <li>Tooltip for sequence associated annotation give name
2932 </ul> <em>Web Services and URL fetching</em>
2934 <li>JPred3 web service</li>
2935 <li>Prototype sequence search client (no public services
2937 <li>Fetch either seed alignment or full alignment from
2939 <li>URL Links created for matching database cross
2940 references as well as sequence ID</li>
2941 <li>URL Links can be created using regular-expressions</li>
2942 </ul> <em>Sequence Database Connectivity</em>
2944 <li>Retrieval of cross-referenced sequences from other
2946 <li>Generalised database reference retrieval and
2947 validation to all fetchable databases</li>
2948 <li>Fetch sequences from DAS sources supporting the
2949 sequence command</li>
2950 </ul> <em>Import and Export</em>
2951 <li>export annotation rows as CSV for spreadsheet import</li>
2952 <li>Jalview projects record alignment dataset associations,
2953 EMBL products, and cDNA sequence mappings</li>
2954 <li>Sequence Group colour can be specified in Annotation
2956 <li>Ad-hoc colouring of group in Annotation File using RGB
2957 triplet as name of colourscheme</li>
2958 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2960 <li>treenode binding for VAMSAS tree exchange</li>
2961 <li>local editing and update of sequences in VAMSAS
2962 alignments (experimental)</li>
2963 <li>Create new or select existing session to join</li>
2964 <li>load and save of vamsas documents</li>
2965 </ul> <em>Application command line</em>
2967 <li>-tree parameter to open trees (introduced for passing
2969 <li>-fetchfrom command line argument to specify nicknames
2970 of DAS servers to query for alignment features</li>
2971 <li>-dasserver command line argument to add new servers
2972 that are also automatically queried for features</li>
2973 <li>-groovy command line argument executes a given groovy
2974 script after all input data has been loaded and parsed</li>
2975 </ul> <em>Applet-Application data exchange</em>
2977 <li>Trees passed as applet parameters can be passed to
2978 application (when using "View in full
2979 application")</li>
2980 </ul> <em>Applet Parameters</em>
2982 <li>feature group display control parameter</li>
2983 <li>debug parameter</li>
2984 <li>showbutton parameter</li>
2985 </ul> <em>Applet API methods</em>
2987 <li>newView public method</li>
2988 <li>Window (current view) specific get/set public methods</li>
2989 <li>Feature display control methods</li>
2990 <li>get list of currently selected sequences</li>
2991 </ul> <em>New Jalview distribution features</em>
2993 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2994 <li>RELEASE file gives build properties for the latest
2995 Jalview release.</li>
2996 <li>Java 1.1 Applet build made easier and donotobfuscate
2997 property controls execution of obfuscator</li>
2998 <li>Build target for generating source distribution</li>
2999 <li>Debug flag for javacc</li>
3000 <li>.jalview_properties file is documented (slightly) in
3001 jalview.bin.Cache</li>
3002 <li>Continuous Build Integration for stable and
3003 development version of Application, Applet and source
3008 <li>selected region output includes visible annotations
3009 (for certain formats)</li>
3010 <li>edit label/displaychar contains existing label/char
3012 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
3013 <li>shorter peptide product names from EMBL records</li>
3014 <li>Newick string generator makes compact representations</li>
3015 <li>bootstrap values parsed correctly for tree files with
3017 <li>pathological filechooser bug avoided by not allowing
3018 filenames containing a ':'</li>
3019 <li>Fixed exception when parsing GFF files containing
3020 global sequence features</li>
3021 <li>Alignment datasets are finalized only when number of
3022 references from alignment sequences goes to zero</li>
3023 <li>Close of tree branch colour box without colour
3024 selection causes cascading exceptions</li>
3025 <li>occasional negative imgwidth exceptions</li>
3026 <li>better reporting of non-fatal warnings to user when
3027 file parsing fails.</li>
3028 <li>Save works when Jalview project is default format</li>
3029 <li>Save as dialog opened if current alignment format is
3030 not a valid output format</li>
3031 <li>UniProt canonical names introduced for both das and
3033 <li>Histidine should be midblue (not pink!) in Zappo</li>
3034 <li>error messages passed up and output when data read
3036 <li>edit undo recovers previous dataset sequence when
3037 sequence is edited</li>
3038 <li>allow PDB files without pdb ID HEADER lines (like
3039 those generated by MODELLER) to be read in properly</li>
3040 <li>allow reading of JPred concise files as a normal
3042 <li>Stockholm annotation parsing and alignment properties
3043 import fixed for PFAM records</li>
3044 <li>Structure view windows have correct name in Desktop
3046 <li>annotation consisting of sequence associated scores
3047 can be read and written correctly to annotation file</li>
3048 <li>Aligned cDNA translation to aligned peptide works
3050 <li>Fixed display of hidden sequence markers and
3051 non-italic font for representatives in Applet</li>
3052 <li>Applet Menus are always embedded in applet window on
3054 <li>Newly shown features appear at top of stack (in
3056 <li>Annotations added via parameter not drawn properly
3057 due to null pointer exceptions</li>
3058 <li>Secondary structure lines are drawn starting from
3059 first column of alignment</li>
3060 <li>UniProt XML import updated for new schema release in
3062 <li>Sequence feature to sequence ID match for Features
3063 file is case-insensitive</li>
3064 <li>Sequence features read from Features file appended to
3065 all sequences with matching IDs</li>
3066 <li>PDB structure coloured correctly for associated views
3067 containing a sub-sequence</li>
3068 <li>PDB files can be retrieved by applet from Jar files</li>
3069 <li>feature and annotation file applet parameters
3070 referring to different directories are retrieved correctly</li>
3071 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3072 <li>Fixed application hang whilst waiting for
3073 splash-screen version check to complete</li>
3074 <li>Applet properly URLencodes input parameter values
3075 when passing them to the launchApp service</li>
3076 <li>display name and local features preserved in results
3077 retrieved from web service</li>
3078 <li>Visual delay indication for sequence retrieval and
3079 sequence fetcher initialisation</li>
3080 <li>updated Application to use DAS 1.53e version of
3081 dasobert DAS client</li>
3082 <li>Re-instated Full AMSA support and .amsa file
3084 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3092 <div align="center">
3093 <strong>2.3</strong><br> 9/5/07
3098 <li>Jmol 11.0.2 integration</li>
3099 <li>PDB views stored in Jalview XML files</li>
3100 <li>Slide sequences</li>
3101 <li>Edit sequence in place</li>
3102 <li>EMBL CDS features</li>
3103 <li>DAS Feature mapping</li>
3104 <li>Feature ordering</li>
3105 <li>Alignment Properties</li>
3106 <li>Annotation Scores</li>
3107 <li>Sort by scores</li>
3108 <li>Feature/annotation editing in applet</li>
3113 <li>Headless state operation in 2.2.1</li>
3114 <li>Incorrect and unstable DNA pairwise alignment</li>
3115 <li>Cut and paste of sequences with annotation</li>
3116 <li>Feature group display state in XML</li>
3117 <li>Feature ordering in XML</li>
3118 <li>blc file iteration selection using filename # suffix</li>
3119 <li>Stockholm alignment properties</li>
3120 <li>Stockhom alignment secondary structure annotation</li>
3121 <li>2.2.1 applet had no feature transparency</li>
3122 <li>Number pad keys can be used in cursor mode</li>
3123 <li>Structure Viewer mirror image resolved</li>
3130 <div align="center">
3131 <strong>2.2.1</strong><br> 12/2/07
3136 <li>Non standard characters can be read and displayed
3137 <li>Annotations/Features can be imported/exported to the
3139 <li>Applet allows editing of sequence/annotation/group
3140 name & description
3141 <li>Preference setting to display sequence name in
3143 <li>Annotation file format extended to allow
3144 Sequence_groups to be defined
3145 <li>Default opening of alignment overview panel can be
3146 specified in preferences
3147 <li>PDB residue numbering annotation added to associated
3153 <li>Applet crash under certain Linux OS with Java 1.6
3155 <li>Annotation file export / import bugs fixed
3156 <li>PNG / EPS image output bugs fixed
3162 <div align="center">
3163 <strong>2.2</strong><br> 27/11/06
3168 <li>Multiple views on alignment
3169 <li>Sequence feature editing
3170 <li>"Reload" alignment
3171 <li>"Save" to current filename
3172 <li>Background dependent text colour
3173 <li>Right align sequence ids
3174 <li>User-defined lower case residue colours
3177 <li>Menu item accelerator keys
3178 <li>Control-V pastes to current alignment
3179 <li>Cancel button for DAS Feature Fetching
3180 <li>PCA and PDB Viewers zoom via mouse roller
3181 <li>User-defined sub-tree colours and sub-tree selection
3183 <li>'New Window' button on the 'Output to Text box'
3188 <li>New memory efficient Undo/Redo System
3189 <li>Optimised symbol lookups and conservation/consensus
3191 <li>Region Conservation/Consensus recalculated after
3193 <li>Fixed Remove Empty Columns Bug (empty columns at end
3195 <li>Slowed DAS Feature Fetching for increased robustness.
3197 <li>Made angle brackets in ASCII feature descriptions
3199 <li>Re-instated Zoom function for PCA
3200 <li>Sequence descriptions conserved in web service
3202 <li>UniProt ID discoverer uses any word separated by
3204 <li>WsDbFetch query/result association resolved
3205 <li>Tree leaf to sequence mapping improved
3206 <li>Smooth fonts switch moved to FontChooser dialog box.
3213 <div align="center">
3214 <strong>2.1.1</strong><br> 12/9/06
3219 <li>Copy consensus sequence to clipboard</li>
3224 <li>Image output - rightmost residues are rendered if
3225 sequence id panel has been resized</li>
3226 <li>Image output - all offscreen group boundaries are
3228 <li>Annotation files with sequence references - all
3229 elements in file are relative to sequence position</li>
3230 <li>Mac Applet users can use Alt key for group editing</li>
3236 <div align="center">
3237 <strong>2.1</strong><br> 22/8/06
3242 <li>MAFFT Multiple Alignment in default Web Service list</li>
3243 <li>DAS Feature fetching</li>
3244 <li>Hide sequences and columns</li>
3245 <li>Export Annotations and Features</li>
3246 <li>GFF file reading / writing</li>
3247 <li>Associate structures with sequences from local PDB
3249 <li>Add sequences to exisiting alignment</li>
3250 <li>Recently opened files / URL lists</li>
3251 <li>Applet can launch the full application</li>
3252 <li>Applet has transparency for features (Java 1.2
3254 <li>Applet has user defined colours parameter</li>
3255 <li>Applet can load sequences from parameter
3256 "sequence<em>x</em>"
3262 <li>Redundancy Panel reinstalled in the Applet</li>
3263 <li>Monospaced font - EPS / rescaling bug fixed</li>
3264 <li>Annotation files with sequence references bug fixed</li>
3270 <div align="center">
3271 <strong>2.08.1</strong><br> 2/5/06
3276 <li>Change case of selected region from Popup menu</li>
3277 <li>Choose to match case when searching</li>
3278 <li>Middle mouse button and mouse movement can compress /
3279 expand the visible width and height of the alignment</li>
3284 <li>Annotation Panel displays complete JNet results</li>
3290 <div align="center">
3291 <strong>2.08b</strong><br> 18/4/06
3297 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3298 <li>Righthand label on wrapped alignments shows correct
3305 <div align="center">
3306 <strong>2.08</strong><br> 10/4/06
3311 <li>Editing can be locked to the selection area</li>
3312 <li>Keyboard editing</li>
3313 <li>Create sequence features from searches</li>
3314 <li>Precalculated annotations can be loaded onto
3316 <li>Features file allows grouping of features</li>
3317 <li>Annotation Colouring scheme added</li>
3318 <li>Smooth fonts off by default - Faster rendering</li>
3319 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3324 <li>Drag & Drop fixed on Linux</li>
3325 <li>Jalview Archive file faster to load/save, sequence
3326 descriptions saved.</li>
3332 <div align="center">
3333 <strong>2.07</strong><br> 12/12/05
3338 <li>PDB Structure Viewer enhanced</li>
3339 <li>Sequence Feature retrieval and display enhanced</li>
3340 <li>Choose to output sequence start-end after sequence
3341 name for file output</li>
3342 <li>Sequence Fetcher WSDBFetch@EBI</li>
3343 <li>Applet can read feature files, PDB files and can be
3344 used for HTML form input</li>
3349 <li>HTML output writes groups and features</li>
3350 <li>Group editing is Control and mouse click</li>
3351 <li>File IO bugs</li>
3357 <div align="center">
3358 <strong>2.06</strong><br> 28/9/05
3363 <li>View annotations in wrapped mode</li>
3364 <li>More options for PCA viewer</li>
3369 <li>GUI bugs resolved</li>
3370 <li>Runs with -nodisplay from command line</li>
3376 <div align="center">
3377 <strong>2.05b</strong><br> 15/9/05
3382 <li>Choose EPS export as lineart or text</li>
3383 <li>Jar files are executable</li>
3384 <li>Can read in Uracil - maps to unknown residue</li>
3389 <li>Known OutOfMemory errors give warning message</li>
3390 <li>Overview window calculated more efficiently</li>
3391 <li>Several GUI bugs resolved</li>
3397 <div align="center">
3398 <strong>2.05</strong><br> 30/8/05
3403 <li>Edit and annotate in "Wrapped" view</li>
3408 <li>Several GUI bugs resolved</li>
3414 <div align="center">
3415 <strong>2.04</strong><br> 24/8/05
3420 <li>Hold down mouse wheel & scroll to change font
3426 <li>Improved JPred client reliability</li>
3427 <li>Improved loading of Jalview files</li>
3433 <div align="center">
3434 <strong>2.03</strong><br> 18/8/05
3439 <li>Set Proxy server name and port in preferences</li>
3440 <li>Multiple URL links from sequence ids</li>
3441 <li>User Defined Colours can have a scheme name and added
3443 <li>Choose to ignore gaps in consensus calculation</li>
3444 <li>Unix users can set default web browser</li>
3445 <li>Runs without GUI for batch processing</li>
3446 <li>Dynamically generated Web Service Menus</li>
3451 <li>InstallAnywhere download for Sparc Solaris</li>
3457 <div align="center">
3458 <strong>2.02</strong><br> 18/7/05
3464 <li>Copy & Paste order of sequences maintains
3465 alignment order.</li>
3471 <div align="center">
3472 <strong>2.01</strong><br> 12/7/05
3477 <li>Use delete key for deleting selection.</li>
3478 <li>Use Mouse wheel to scroll sequences.</li>
3479 <li>Help file updated to describe how to add alignment
3481 <li>Version and build date written to build properties
3483 <li>InstallAnywhere installation will check for updates
3484 at launch of Jalview.</li>
3489 <li>Delete gaps bug fixed.</li>
3490 <li>FileChooser sorts columns.</li>
3491 <li>Can remove groups one by one.</li>
3492 <li>Filechooser icons installed.</li>
3493 <li>Finder ignores return character when searching.
3494 Return key will initiate a search.<br>
3501 <div align="center">
3502 <strong>2.0</strong><br> 20/6/05
3507 <li>New codebase</li>