3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Release History</title>
26 /* remove bullets, narrower indent */
27 list-style-type: none;
34 /* separate the items from eachother */
41 /* doesnt get processed in javahelp */
50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
77 <td><div align="left">
81 <!-- JAL-2588 -->Show gaps in overview window by colouring
82 in grey (sequences used to be coloured grey, and gaps were
86 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
90 <!-- JAL-2587 -->Overview updates immediately on increase
91 in size and progress bar shown as higher resolution
92 overview is recalculated
97 <td><div align="left">
101 <!-- JAL-2664 -->Overview window redraws every hidden
102 column region row by row
105 <!-- JAL-2681 -->duplicate protein sequences shown after
106 retrieving Ensembl crossrefs for sequences from Uniprot
109 <!-- JAL-2603 -->Overview window throws NPE if show boxes
110 format setting is unticked
113 <!-- JAL-2610 -->Groups are coloured wrongly in overview
114 if group has show boxes format setting unticked
117 <!-- JAL-2672,JAL-2665 -->Redraw problems when
118 autoscrolling whilst dragging current selection group to
119 include sequences and columns not currently displayed
122 <!-- JAL-2691 -->Not all chains are mapped when multimeric
123 assemblies are imported via CIF file
129 <td width="60" nowrap>
131 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
134 <td><div align="left">
135 <em>Calculations</em>
139 <!-- JAL-1933 -->Occupancy annotation row shows number of
140 ungapped positions in each column of the alignment.
143 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
144 a calculation dialog box
147 <!-- JAL-2379 -->Revised implementation of PCA for speed
148 and memory efficiency (~30x faster)
151 <!-- JAL-2403 -->Revised implementation of sequence
152 similarity scores as used by Tree, PCA, Shading Consensus
153 and other calculations
156 <!-- JAL-2416 -->Score matrices are stored as resource
157 files within the Jalview codebase
160 <!-- JAL-2500 -->Trees computed on Sequence Feature
161 Similarity may have different topology due to increased
168 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
169 model for alignments and groups
172 <!-- JAL-384 -->Custom shading schemes created via groovy
179 <!-- JAL-2526 -->Efficiency improvements for interacting
180 with alignment and overview windows
183 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
187 <!-- JAL-2388 -->Hidden columns and sequences can be
191 <!-- JAL-2611 -->Click-drag in visible area allows fine
192 adjustment of visible position
196 <em>Data import/export</em>
199 <!-- JAL-2535 -->Posterior probability annotation from
200 Stockholm files imported as sequence associated annotation
203 <!-- JAL-2507 -->More robust per-sequence positional
204 annotation input/output via stockholm flatfile
207 <!-- JAL-2533 -->Sequence names don't include file
208 extension when importing structure files without embedded
209 names or PDB accessions
212 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
213 format sequence substitution matrices
216 <em>User Interface</em>
219 <!-- JAL-2447 --> Experimental Features Checkbox in
220 Desktop's Tools menu to hide or show untested features in
224 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
225 via Overview or sequence motif search operations
228 <!-- JAL-2547 -->Amend sequence features dialog box can be
229 opened by double clicking gaps within sequence feature
233 <!-- JAL-1476 -->Status bar message shown when not enough
234 aligned positions were available to create a 3D structure
238 <em>3D Structure</em>
241 <!-- JAL-2430 -->Hidden regions in alignment views are not
242 coloured in linked structure views
245 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
246 file-based command exchange
249 <!-- JAL-2375 -->Structure chooser automatically shows
250 Cached Structures rather than querying the PDBe if
251 structures are already available for sequences
254 <!-- JAL-2520 -->Structures imported via URL are cached in
255 the Jalview project rather than downloaded again when the
259 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
260 to transfer Chimera's structure attributes as Jalview
261 features, and vice-versa (<strong>Experimental
265 <em>Web Services</em>
268 <!-- JAL-2549 -->Updated JABAWS client to v2.2
271 <!-- JAL-2335 -->Filter non-standard amino acids and
272 nucleotides when submitting to AACon and other MSA
276 <!-- JAL-2316, -->URLs for viewing database
277 cross-references provided by identifiers.org and the
285 <!-- JAL-2344 -->FileFormatI interface for describing and
286 identifying file formats (instead of String constants)
289 <!-- JAL-2228 -->FeatureCounter script refactored for
290 efficiency when counting all displayed features (not
291 backwards compatible with 2.10.1)
294 <em>Example files</em>
297 <!-- JAL-2631 -->Graduated feature colour style example
298 included in the example feature file
301 <em>Documentation</em>
304 <!-- JAL-2339 -->Release notes reformatted for readability
305 with the built-in Java help viewer
308 <!-- JAL-1644 -->Find documentation updated with 'search
309 sequence description' option
315 <!-- JAL-2485, -->External service integration tests for
316 Uniprot REST Free Text Search Client
319 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
322 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
327 <td><div align="left">
328 <em>Calculations</em>
331 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
332 matrix - C->R should be '-3'<br />Old matrix restored
333 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
335 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
336 Jalview's treatment of gaps in PCA and substitution matrix
337 based Tree calculations.<br /> <br />In earlier versions
338 of Jalview, gaps matching gaps were penalised, and gaps
339 matching non-gaps penalised even more. In the PCA
340 calculation, gaps were actually treated as non-gaps - so
341 different costs were applied, which meant Jalview's PCAs
342 were different to those produced by SeqSpace.<br />Jalview
343 now treats gaps in the same way as SeqSpace (ie it scores
344 them as 0). <br /> <br />Enter the following in the
345 Groovy console to restore pre-2.10.2 behaviour:<br />
346 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
347 // for 2.10.1 mode <br />
348 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
349 // to restore 2.10.2 mode <br /> <br /> <em>Note:
350 these settings will affect all subsequent tree and PCA
351 calculations (not recommended)</em></li>
353 <!-- JAL-2424 -->Fixed off-by-one bug that affected
354 scaling of branch lengths for trees computed using
355 Sequence Feature Similarity.
358 <!-- JAL-2377 -->PCA calculation could hang when
359 generating output report when working with highly
363 <!-- JAL-2544 --> Sort by features includes features to
364 right of selected region when gaps present on right-hand
368 <em>User Interface</em>
371 <!-- JAL-2346 -->Reopening Colour by annotation dialog
372 doesn't reselect a specific sequence's associated
373 annotation after it was used for colouring a view
376 <!-- JAL-2419 -->Current selection lost if popup menu
377 opened on a region of alignment without groups
380 <!-- JAL-2374 -->Popup menu not always shown for regions
381 of an alignment with overlapping groups
384 <!-- JAL-2310 -->Finder double counts if both a sequence's
385 name and description match
388 <!-- JAL-2370 -->Hiding column selection containing two
389 hidden regions results in incorrect hidden regions
392 <!-- JAL-2386 -->'Apply to all groups' setting when
393 changing colour does not apply Conservation slider value
397 <!-- JAL-2373 -->Percentage identity and conservation menu
398 items do not show a tick or allow shading to be disabled
401 <!-- JAL-2385 -->Conservation shading or PID threshold
402 lost when base colourscheme changed if slider not visible
405 <!-- JAL-2547 -->Sequence features shown in tooltip for
406 gaps before start of features
409 <!-- JAL-2623 -->Graduated feature colour threshold not
410 restored to UI when feature colour is edited
413 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
414 a time when scrolling vertically in wrapped mode.
417 <!-- JAL-2630 -->Structure and alignment overview update
418 as graduate feature colour settings are modified via the
422 <!-- JAL-2034 -->Overview window doesn't always update
423 when a group defined on the alignment is resized
426 <!-- JAL-2605 -->Mouseovers on left/right scale region in
427 wrapped view result in positional status updates
431 <!-- JAL-2563 -->Status bar doesn't show position for
432 ambiguous amino acid and nucleotide symbols
435 <!-- JAL-2602 -->Copy consensus sequence failed if
436 alignment included gapped columns
439 <!-- JAL-2473 -->Minimum size set for Jalview windows so
440 widgets don't permanently disappear
443 <!-- JAL-2503 -->Cannot select or filter quantitative
444 annotation that are shown only as column labels (e.g.
445 T-Coffee column reliability scores)
448 <!-- JAL-2594 -->Exception thrown if trying to create a
449 sequence feature on gaps only
452 <!-- JAL-2504 -->Features created with 'New feature'
453 button from a Find inherit previously defined feature type
454 rather than the Find query string
457 <!-- JAL-2423 -->incorrect title in output window when
458 exporting tree calculated in Jalview
461 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
462 and then revealing them reorders sequences on the
466 <!-- JAL-964 -->Group panel in sequence feature settings
467 doesn't update to reflect available set of groups after
468 interactively adding or modifying features
471 <!-- JAL-2225 -->Sequence Database chooser unusable on
475 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
476 only excluded gaps in current sequence and ignored
483 <!-- JAL-2421 -->Overview window visible region moves
484 erratically when hidden rows or columns are present
487 <!-- JAL-2362 -->Per-residue colourschemes applied via the
488 Structure Viewer's colour menu don't correspond to
492 <!-- JAL-2405 -->Protein specific colours only offered in
493 colour and group colour menu for protein alignments
496 <!-- JAL-2385 -->Colour threshold slider doesn't update to
497 reflect currently selected view or group's shading
501 <!-- JAL-2624 -->Feature colour thresholds not respected
502 when rendered on overview and structures when opacity at
506 <!-- JAL-2589 -->User defined gap colour not shown in
507 overview when features overlaid on alignment
510 <em>Data import/export</em>
513 <!-- JAL-2576 -->Very large alignments take a long time to
517 <!-- JAL-2507 -->Per-sequence RNA secondary structures
518 added after a sequence was imported are not written to
522 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
523 when importing RNA secondary structure via Stockholm
526 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
527 not shown in correct direction for simple pseudoknots
530 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
531 with lightGray or darkGray via features file (but can
535 <!-- JAL-2383 -->Above PID colour threshold not recovered
536 when alignment view imported from project
539 <!-- JAL-2520,JAL-2465 -->No mappings generated between
540 structure and sequences extracted from structure files
541 imported via URL and viewed in Jmol
544 <!-- JAL-2520 -->Structures loaded via URL are saved in
545 Jalview Projects rather than fetched via URL again when
546 the project is loaded and the structure viewed
549 <em>Web Services</em>
552 <!-- JAL-2519 -->EnsemblGenomes example failing after
553 release of Ensembl v.88
556 <!-- JAL-2366 -->Proxy server address and port always
557 appear enabled in Preferences->Connections
560 <!-- JAL-2461 -->DAS registry not found exceptions
561 removed from console output
564 <!-- JAL-2582 -->Cannot retrieve protein products from
565 Ensembl by Peptide ID
568 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
569 created from SIFTs, and spurious 'Couldn't open structure
570 in Chimera' errors raised after April 2017 update (problem
571 due to 'null' string rather than empty string used for
572 residues with no corresponding PDB mapping).
575 <em>Application UI</em>
578 <!-- JAL-2361 -->User Defined Colours not added to Colour
582 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
583 case' residues (button in colourscheme editor debugged and
584 new documentation and tooltips added)
587 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
588 doesn't restore group-specific text colour thresholds
591 <!-- JAL-2243 -->Feature settings panel does not update as
592 new features are added to alignment
595 <!-- JAL-2532 -->Cancel in feature settings reverts
596 changes to feature colours via the Amend features dialog
599 <!-- JAL-2506 -->Null pointer exception when attempting to
600 edit graduated feature colour via amend features dialog
604 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
605 selection menu changes colours of alignment views
608 <!-- JAL-2426 -->Spurious exceptions in console raised
609 from alignment calculation workers after alignment has
613 <!-- JAL-1608 -->Typo in selection popup menu - Create
614 groups now 'Create Group'
617 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
618 Create/Undefine group doesn't always work
621 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
622 shown again after pressing 'Cancel'
625 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
626 adjusts start position in wrap mode
629 <!-- JAL-2563 -->Status bar doesn't show positions for
630 ambiguous amino acids
633 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
634 CDS/Protein view after CDS sequences added for aligned
638 <!-- JAL-2592 -->User defined colourschemes called 'User
639 Defined' don't appear in Colours menu
645 <!-- JAL-2468 -->Switching between Nucleotide and Protein
646 score models doesn't always result in an updated PCA plot
649 <!-- JAL-2442 -->Features not rendered as transparent on
650 overview or linked structure view
653 <!-- JAL-2372 -->Colour group by conservation doesn't
657 <!-- JAL-2517 -->Hitting Cancel after applying
658 user-defined colourscheme doesn't restore original
665 <!-- JAL-2314 -->Unit test failure:
666 jalview.ws.jabaws.RNAStructExportImport setup fails
669 <!-- JAL-2307 -->Unit test failure:
670 jalview.ws.sifts.SiftsClientTest due to compatibility
671 problems with deep array comparison equality asserts in
672 successive versions of TestNG
675 <!-- JAL-2479 -->Relocated StructureChooserTest and
676 ParameterUtilsTest Unit tests to Network suite
679 <em>New Known Issues</em>
682 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
683 phase after a sequence motif find operation
686 <!-- JAL-2550 -->Importing annotation file with rows
687 containing just upper and lower case letters are
688 interpreted as WUSS RNA secondary structure symbols
691 <!-- JAL-2590 -->Cannot load and display Newick trees
692 reliably from eggnog Ortholog database
695 <!-- JAL-2468 -->Status bar shows 'Marked x columns
696 containing features of type Highlight' when 'B' is pressed
697 to mark columns containing highlighted regions.
700 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
701 doesn't always add secondary structure annotation.
706 <td width="60" nowrap>
708 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
711 <td><div align="left">
715 <!-- JAL-98 -->Improved memory usage: sparse arrays used
716 for all consensus calculations
719 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
722 <li>Updated Jalview's Certum code signing certificate
728 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
729 set of database cross-references, sorted alphabetically
732 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
733 from database cross references. Users with custom links
734 will receive a <a href="webServices/urllinks.html#warning">warning
735 dialog</a> asking them to update their preferences.
738 <!-- JAL-2287-->Cancel button and escape listener on
739 dialog warning user about disconnecting Jalview from a
743 <!-- JAL-2320-->Jalview's Chimera control window closes if
744 the Chimera it is connected to is shut down
747 <!-- JAL-1738-->New keystroke (B) and Select highlighted
748 columns menu item to mark columns containing highlighted
749 regions (e.g. from structure selections or results of a
753 <!-- JAL-2284-->Command line option for batch-generation
754 of HTML pages rendering alignment data with the BioJS
764 <!-- JAL-2286 -->Columns with more than one modal residue
765 are not coloured or thresholded according to percent
766 identity (first observed in Jalview 2.8.2)
769 <!-- JAL-2301 -->Threonine incorrectly reported as not
773 <!-- JAL-2318 -->Updates to documentation pages (above PID
774 threshold, amino acid properties)
777 <!-- JAL-2292 -->Lower case residues in sequences are not
778 reported as mapped to residues in a structure file in the
782 <!--JAL-2324 -->Identical features with non-numeric scores
783 could be added multiple times to a sequence
786 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
787 bond features shown as two highlighted residues rather
788 than a range in linked structure views, and treated
789 correctly when selecting and computing trees from features
792 <!-- JAL-2281-->Custom URL links for database
793 cross-references are matched to database name regardless
801 <!-- JAL-2282-->Custom URL links for specific database
802 names without regular expressions also offer links from
806 <!-- JAL-2315-->Removing a single configured link in the
807 URL links pane in Connections preferences doesn't actually
808 update Jalview configuration
811 <!-- JAL-2272-->CTRL-Click on a selected region to open
812 the alignment area popup menu doesn't work on El-Capitan
815 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
816 files with similarly named sequences if dropped onto the
820 <!-- JAL-2312 -->Additional mappings are shown for PDB
821 entries where more chains exist in the PDB accession than
822 are reported in the SIFTS file
825 <!-- JAL-2317-->Certain structures do not get mapped to
826 the structure view when displayed with Chimera
829 <!-- JAL-2317-->No chains shown in the Chimera view
830 panel's View->Show Chains submenu
833 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
834 work for wrapped alignment views
837 <!--JAL-2197 -->Rename UI components for running JPred
838 predictions from 'JNet' to 'JPred'
841 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
842 corrupted when annotation panel vertical scroll is not at
846 <!--JAL-2332 -->Attempting to view structure for Hen
847 lysozyme results in a PDB Client error dialog box
850 <!-- JAL-2319 -->Structure View's mapping report switched
851 ranges for PDB and sequence for SIFTS
854 SIFTS 'Not_Observed' residues mapped to non-existant
858 <!-- <em>New Known Issues</em>
865 <td width="60" nowrap>
867 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
868 <em>25/10/2016</em></strong>
871 <td><em>Application</em>
873 <li>3D Structure chooser opens with 'Cached structures'
874 view if structures already loaded</li>
875 <li>Progress bar reports models as they are loaded to
882 <li>Colour by conservation always enabled and no tick
883 shown in menu when BLOSUM or PID shading applied</li>
884 <li>FER1_ARATH and FER2_ARATH labels were switched in
885 example sequences/projects/trees</li>
889 <li>Jalview projects with views of local PDB structure
890 files saved on Windows cannot be opened on OSX</li>
891 <li>Multiple structure views can be opened and superposed
892 without timeout for structures with multiple models or
893 multiple sequences in alignment</li>
894 <li>Cannot import or associated local PDB files without a
895 PDB ID HEADER line</li>
896 <li>RMSD is not output in Jmol console when superposition
898 <li>Drag and drop of URL from Browser fails for Linux and
899 OSX versions earlier than El Capitan</li>
900 <li>ENA client ignores invalid content from ENA server</li>
901 <li>Exceptions are not raised in console when ENA client
902 attempts to fetch non-existent IDs via Fetch DB Refs UI
904 <li>Exceptions are not raised in console when a new view
905 is created on the alignment</li>
906 <li>OSX right-click fixed for group selections: CMD-click
907 to insert/remove gaps in groups and CTRL-click to open group
910 <em>Build and deployment</em>
912 <li>URL link checker now copes with multi-line anchor
915 <em>New Known Issues</em>
917 <li>Drag and drop from URL links in browsers do not work
924 <td width="60" nowrap>
926 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
932 <!-- JAL-2124 -->Updated Spanish translations.
935 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
936 for importing structure data to Jalview. Enables mmCIF and
940 <!-- JAL-192 --->Alignment ruler shows positions relative to
944 <!-- JAL-2202 -->Position/residue shown in status bar when
945 mousing over sequence associated annotation
948 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
952 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
953 '()', canonical '[]' and invalid '{}' base pair populations
957 <!-- JAL-2092 -->Feature settings popup menu options for
958 showing or hiding columns containing a feature
961 <!-- JAL-1557 -->Edit selected group by double clicking on
962 group and sequence associated annotation labels
965 <!-- JAL-2236 -->Sequence name added to annotation label in
966 select/hide columns by annotation and colour by annotation
970 </ul> <em>Application</em>
973 <!-- JAL-2050-->Automatically hide introns when opening a
977 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
981 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
982 structure mappings with the EMBL-EBI PDBe SIFTS database
985 <!-- JAL-2079 -->Updated download sites used for Rfam and
986 Pfam sources to xfam.org
989 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
992 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
993 over sequences in Jalview
996 <!-- JAL-2027-->Support for reverse-complement coding
997 regions in ENA and EMBL
1000 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
1001 for record retrieval via ENA rest API
1004 <!-- JAL-2027 -->Support for ENA CDS records with reverse
1008 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
1009 groovy script execution
1012 <!-- JAL-1812 -->New 'execute Groovy script' option in an
1013 alignment window's Calculate menu
1016 <!-- JAL-1812 -->Allow groovy scripts that call
1017 Jalview.getAlignFrames() to run in headless mode
1020 <!-- JAL-2068 -->Support for creating new alignment
1021 calculation workers from groovy scripts
1024 <!-- JAL-1369 --->Store/restore reference sequence in
1028 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1029 associations are now saved/restored from project
1032 <!-- JAL-1993 -->Database selection dialog always shown
1033 before sequence fetcher is opened
1036 <!-- JAL-2183 -->Double click on an entry in Jalview's
1037 database chooser opens a sequence fetcher
1040 <!-- JAL-1563 -->Free-text search client for UniProt using
1041 the UniProt REST API
1044 <!-- JAL-2168 -->-nonews command line parameter to prevent
1045 the news reader opening
1048 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1049 querying stored in preferences
1052 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1056 <!-- JAL-1977-->Tooltips shown on database chooser
1059 <!-- JAL-391 -->Reverse complement function in calculate
1060 menu for nucleotide sequences
1063 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1064 and feature counts preserves alignment ordering (and
1065 debugged for complex feature sets).
1068 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1069 viewing structures with Jalview 2.10
1072 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1073 genome, transcript CCDS and gene ids via the Ensembl and
1074 Ensembl Genomes REST API
1077 <!-- JAL-2049 -->Protein sequence variant annotation
1078 computed for 'sequence_variant' annotation on CDS regions
1082 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1086 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1087 Ref Fetcher fails to match, or otherwise updates sequence
1088 data from external database records.
1091 <!-- JAL-2154 -->Revised Jalview Project format for
1092 efficient recovery of sequence coding and alignment
1093 annotation relationships.
1095 </ul> <!-- <em>Applet</em>
1106 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1110 <!-- JAL-2018-->Export features in Jalview format (again)
1111 includes graduated colourschemes
1114 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1115 working with big alignments and lots of hidden columns
1118 <!-- JAL-2053-->Hidden column markers not always rendered
1119 at right of alignment window
1122 <!-- JAL-2067 -->Tidied up links in help file table of
1126 <!-- JAL-2072 -->Feature based tree calculation not shown
1130 <!-- JAL-2075 -->Hidden columns ignored during feature
1131 based tree calculation
1134 <!-- JAL-2065 -->Alignment view stops updating when show
1135 unconserved enabled for group on alignment
1138 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1142 <!-- JAL-2146 -->Alignment column in status incorrectly
1143 shown as "Sequence position" when mousing over
1147 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1148 hidden columns present
1151 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1152 user created annotation added to alignment
1155 <!-- JAL-1841 -->RNA Structure consensus only computed for
1156 '()' base pair annotation
1159 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1160 in zero scores for all base pairs in RNA Structure
1164 <!-- JAL-2174-->Extend selection with columns containing
1168 <!-- JAL-2275 -->Pfam format writer puts extra space at
1169 beginning of sequence
1172 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1176 <!-- JAL-2238 -->Cannot create groups on an alignment from
1177 from a tree when t-coffee scores are shown
1180 <!-- JAL-1836,1967 -->Cannot import and view PDB
1181 structures with chains containing negative resnums (4q4h)
1184 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1188 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1189 to Clustal, PIR and PileUp output
1192 <!-- JAL-2008 -->Reordering sequence features that are
1193 not visible causes alignment window to repaint
1196 <!-- JAL-2006 -->Threshold sliders don't work in
1197 graduated colour and colour by annotation row for e-value
1198 scores associated with features and annotation rows
1201 <!-- JAL-1797 -->amino acid physicochemical conservation
1202 calculation should be case independent
1205 <!-- JAL-2173 -->Remove annotation also updates hidden
1209 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1210 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1211 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1214 <!-- JAL-2065 -->Null pointer exceptions and redraw
1215 problems when reference sequence defined and 'show
1216 non-conserved' enabled
1219 <!-- JAL-1306 -->Quality and Conservation are now shown on
1220 load even when Consensus calculation is disabled
1223 <!-- JAL-1932 -->Remove right on penultimate column of
1224 alignment does nothing
1227 <em>Application</em>
1230 <!-- JAL-1552-->URLs and links can't be imported by
1231 drag'n'drop on OSX when launched via webstart (note - not
1232 yet fixed for El Capitan)
1235 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1236 output when running on non-gb/us i18n platforms
1239 <!-- JAL-1944 -->Error thrown when exporting a view with
1240 hidden sequences as flat-file alignment
1243 <!-- JAL-2030-->InstallAnywhere distribution fails when
1247 <!-- JAL-2080-->Jalview very slow to launch via webstart
1248 (also hotfix for 2.9.0b2)
1251 <!-- JAL-2085 -->Cannot save project when view has a
1252 reference sequence defined
1255 <!-- JAL-1011 -->Columns are suddenly selected in other
1256 alignments and views when revealing hidden columns
1259 <!-- JAL-1989 -->Hide columns not mirrored in complement
1260 view in a cDNA/Protein splitframe
1263 <!-- JAL-1369 -->Cannot save/restore representative
1264 sequence from project when only one sequence is
1268 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1269 in Structure Chooser
1272 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1273 structure consensus didn't refresh annotation panel
1276 <!-- JAL-1962 -->View mapping in structure view shows
1277 mappings between sequence and all chains in a PDB file
1280 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1281 dialogs format columns correctly, don't display array
1282 data, sort columns according to type
1285 <!-- JAL-1975 -->Export complete shown after destination
1286 file chooser is cancelled during an image export
1289 <!-- JAL-2025 -->Error when querying PDB Service with
1290 sequence name containing special characters
1293 <!-- JAL-2024 -->Manual PDB structure querying should be
1297 <!-- JAL-2104 -->Large tooltips with broken HTML
1298 formatting don't wrap
1301 <!-- JAL-1128 -->Figures exported from wrapped view are
1302 truncated so L looks like I in consensus annotation
1305 <!-- JAL-2003 -->Export features should only export the
1306 currently displayed features for the current selection or
1310 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1311 after fetching cross-references, and restoring from
1315 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1316 followed in the structure viewer
1319 <!-- JAL-2163 -->Titles for individual alignments in
1320 splitframe not restored from project
1323 <!-- JAL-2145 -->missing autocalculated annotation at
1324 trailing end of protein alignment in transcript/product
1325 splitview when pad-gaps not enabled by default
1328 <!-- JAL-1797 -->amino acid physicochemical conservation
1332 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1333 article has been read (reopened issue due to
1334 internationalisation problems)
1337 <!-- JAL-1960 -->Only offer PDB structures in structure
1338 viewer based on sequence name, PDB and UniProt
1343 <!-- JAL-1976 -->No progress bar shown during export of
1347 <!-- JAL-2213 -->Structures not always superimposed after
1348 multiple structures are shown for one or more sequences.
1351 <!-- JAL-1370 -->Reference sequence characters should not
1352 be replaced with '.' when 'Show unconserved' format option
1356 <!-- JAL-1823 -->Cannot specify chain code when entering
1357 specific PDB id for sequence
1360 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1361 'Export hidden sequences' is enabled, but 'export hidden
1362 columns' is disabled.
1365 <!--JAL-2026-->Best Quality option in structure chooser
1366 selects lowest rather than highest resolution structures
1370 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1371 to sequence mapping in 'View Mappings' report
1374 <!-- JAL-2284 -->Unable to read old Jalview projects that
1375 contain non-XML data added after Jalvew wrote project.
1378 <!-- JAL-2118 -->Newly created annotation row reorders
1379 after clicking on it to create new annotation for a
1382 <!-- may exclude, this is an external service stability issue JAL-1941
1383 -- > RNA 3D structure not added via DSSR service</li> -->
1388 <!-- JAL-2151 -->Incorrect columns are selected when
1389 hidden columns present before start of sequence
1392 <!-- JAL-1986 -->Missing dependencies on applet pages
1396 <!-- JAL-1947 -->Overview pixel size changes when
1397 sequences are hidden in applet
1400 <!-- JAL-1996 -->Updated instructions for applet
1401 deployment on examples pages.
1408 <td width="60" nowrap>
1409 <div align="center">
1410 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1411 <em>16/10/2015</em></strong>
1414 <td><em>General</em>
1416 <li>Time stamps for signed Jalview application and applet
1421 <em>Application</em>
1423 <li>Duplicate group consensus and conservation rows
1424 shown when tree is partitioned</li>
1425 <li>Erratic behaviour when tree partitions made with
1426 multiple cDNA/Protein split views</li>
1432 <td width="60" nowrap>
1433 <div align="center">
1434 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1435 <em>8/10/2015</em></strong>
1438 <td><em>General</em>
1440 <li>Updated Spanish translations of localized text for
1442 </ul> <em>Application</em>
1444 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1445 <li>Signed OSX InstallAnywhere installer<br></li>
1446 <li>Support for per-sequence based annotations in BioJSON</li>
1447 </ul> <em>Applet</em>
1449 <li>Split frame example added to applet examples page</li>
1450 </ul> <em>Build and Deployment</em>
1453 <!-- JAL-1888 -->New ant target for running Jalview's test
1461 <li>Mapping of cDNA to protein in split frames
1462 incorrect when sequence start > 1</li>
1463 <li>Broken images in filter column by annotation dialog
1465 <li>Feature colours not parsed from features file</li>
1466 <li>Exceptions and incomplete link URLs recovered when
1467 loading a features file containing HTML tags in feature
1471 <em>Application</em>
1473 <li>Annotations corrupted after BioJS export and
1475 <li>Incorrect sequence limits after Fetch DB References
1476 with 'trim retrieved sequences'</li>
1477 <li>Incorrect warning about deleting all data when
1478 deleting selected columns</li>
1479 <li>Patch to build system for shipping properly signed
1480 JNLP templates for webstart launch</li>
1481 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1482 unreleased structures for download or viewing</li>
1483 <li>Tab/space/return keystroke operation of EMBL-PDBe
1484 fetcher/viewer dialogs works correctly</li>
1485 <li>Disabled 'minimise' button on Jalview windows
1486 running on OSX to workaround redraw hang bug</li>
1487 <li>Split cDNA/Protein view position and geometry not
1488 recovered from jalview project</li>
1489 <li>Initial enabled/disabled state of annotation menu
1490 sorter 'show autocalculated first/last' corresponds to
1492 <li>Restoring of Clustal, RNA Helices and T-Coffee
1493 color schemes from BioJSON</li>
1497 <li>Reorder sequences mirrored in cDNA/Protein split
1499 <li>Applet with Jmol examples not loading correctly</li>
1505 <td><div align="center">
1506 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1508 <td><em>General</em>
1510 <li>Linked visualisation and analysis of DNA and Protein
1513 <li>Translated cDNA alignments shown as split protein
1514 and DNA alignment views</li>
1515 <li>Codon consensus annotation for linked protein and
1516 cDNA alignment views</li>
1517 <li>Link cDNA or Protein product sequences by loading
1518 them onto Protein or cDNA alignments</li>
1519 <li>Reconstruct linked cDNA alignment from aligned
1520 protein sequences</li>
1523 <li>Jmol integration updated to Jmol v14.2.14</li>
1524 <li>Import and export of Jalview alignment views as <a
1525 href="features/bioJsonFormat.html">BioJSON</a></li>
1526 <li>New alignment annotation file statements for
1527 reference sequences and marking hidden columns</li>
1528 <li>Reference sequence based alignment shading to
1529 highlight variation</li>
1530 <li>Select or hide columns according to alignment
1532 <li>Find option for locating sequences by description</li>
1533 <li>Conserved physicochemical properties shown in amino
1534 acid conservation row</li>
1535 <li>Alignments can be sorted by number of RNA helices</li>
1536 </ul> <em>Application</em>
1538 <li>New cDNA/Protein analysis capabilities
1540 <li>Get Cross-References should open a Split Frame
1541 view with cDNA/Protein</li>
1542 <li>Detect when nucleotide sequences and protein
1543 sequences are placed in the same alignment</li>
1544 <li>Split cDNA/Protein views are saved in Jalview
1549 <li>Use REST API to talk to Chimera</li>
1550 <li>Selected regions in Chimera are highlighted in linked
1551 Jalview windows</li>
1553 <li>VARNA RNA viewer updated to v3.93</li>
1554 <li>VARNA views are saved in Jalview Projects</li>
1555 <li>Pseudoknots displayed as Jalview RNA annotation can
1556 be shown in VARNA</li>
1558 <li>Make groups for selection uses marked columns as well
1559 as the active selected region</li>
1561 <li>Calculate UPGMA and NJ trees using sequence feature
1563 <li>New Export options
1565 <li>New Export Settings dialog to control hidden
1566 region export in flat file generation</li>
1568 <li>Export alignment views for display with the <a
1569 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1571 <li>Export scrollable SVG in HTML page</li>
1572 <li>Optional embedding of BioJSON data when exporting
1573 alignment figures to HTML</li>
1575 <li>3D structure retrieval and display
1577 <li>Free text and structured queries with the PDBe
1579 <li>PDBe Search API based discovery and selection of
1580 PDB structures for a sequence set</li>
1584 <li>JPred4 employed for protein secondary structure
1586 <li>Hide Insertions menu option to hide unaligned columns
1587 for one or a group of sequences</li>
1588 <li>Automatically hide insertions in alignments imported
1589 from the JPred4 web server</li>
1590 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1591 system on OSX<br />LGPL libraries courtesy of <a
1592 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1594 <li>changed 'View nucleotide structure' submenu to 'View
1595 VARNA 2D Structure'</li>
1596 <li>change "View protein structure" menu option to "3D
1599 </ul> <em>Applet</em>
1601 <li>New layout for applet example pages</li>
1602 <li>New parameters to enable SplitFrame view
1603 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1604 <li>New example demonstrating linked viewing of cDNA and
1605 Protein alignments</li>
1606 </ul> <em>Development and deployment</em>
1608 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1609 <li>Include installation type and git revision in build
1610 properties and console log output</li>
1611 <li>Jalview Github organisation, and new github site for
1612 storing BioJsMSA Templates</li>
1613 <li>Jalview's unit tests now managed with TestNG</li>
1616 <!-- <em>General</em>
1618 </ul> --> <!-- issues resolved --> <em>Application</em>
1620 <li>Escape should close any open find dialogs</li>
1621 <li>Typo in select-by-features status report</li>
1622 <li>Consensus RNA secondary secondary structure
1623 predictions are not highlighted in amber</li>
1624 <li>Missing gap character in v2.7 example file means
1625 alignment appears unaligned when pad-gaps is not enabled</li>
1626 <li>First switch to RNA Helices colouring doesn't colour
1627 associated structure views</li>
1628 <li>ID width preference option is greyed out when auto
1629 width checkbox not enabled</li>
1630 <li>Stopped a warning dialog from being shown when
1631 creating user defined colours</li>
1632 <li>'View Mapping' in structure viewer shows sequence
1633 mappings for just that viewer's sequences</li>
1634 <li>Workaround for superposing PDB files containing
1635 multiple models in Chimera</li>
1636 <li>Report sequence position in status bar when hovering
1637 over Jmol structure</li>
1638 <li>Cannot output gaps as '.' symbols with Selection ->
1639 output to text box</li>
1640 <li>Flat file exports of alignments with hidden columns
1641 have incorrect sequence start/end</li>
1642 <li>'Aligning' a second chain to a Chimera structure from
1644 <li>Colour schemes applied to structure viewers don't
1645 work for nucleotide</li>
1646 <li>Loading/cut'n'pasting an empty or invalid file leads
1647 to a grey/invisible alignment window</li>
1648 <li>Exported Jpred annotation from a sequence region
1649 imports to different position</li>
1650 <li>Space at beginning of sequence feature tooltips shown
1651 on some platforms</li>
1652 <li>Chimera viewer 'View | Show Chain' menu is not
1654 <li>'New View' fails with a Null Pointer Exception in
1655 console if Chimera has been opened</li>
1656 <li>Mouseover to Chimera not working</li>
1657 <li>Miscellaneous ENA XML feature qualifiers not
1659 <li>NPE in annotation renderer after 'Extract Scores'</li>
1660 <li>If two structures in one Chimera window, mouseover of
1661 either sequence shows on first structure</li>
1662 <li>'Show annotations' options should not make
1663 non-positional annotations visible</li>
1664 <li>Subsequence secondary structure annotation not shown
1665 in right place after 'view flanking regions'</li>
1666 <li>File Save As type unset when current file format is
1668 <li>Save as '.jar' option removed for saving Jalview
1670 <li>Colour by Sequence colouring in Chimera more
1672 <li>Cannot 'add reference annotation' for a sequence in
1673 several views on same alignment</li>
1674 <li>Cannot show linked products for EMBL / ENA records</li>
1675 <li>Jalview's tooltip wraps long texts containing no
1677 </ul> <em>Applet</em>
1679 <li>Jmol to JalviewLite mouseover/link not working</li>
1680 <li>JalviewLite can't import sequences with ID
1681 descriptions containing angle brackets</li>
1682 </ul> <em>General</em>
1684 <li>Cannot export and reimport RNA secondary structure
1685 via jalview annotation file</li>
1686 <li>Random helix colour palette for colour by annotation
1687 with RNA secondary structure</li>
1688 <li>Mouseover to cDNA from STOP residue in protein
1689 translation doesn't work.</li>
1690 <li>hints when using the select by annotation dialog box</li>
1691 <li>Jmol alignment incorrect if PDB file has alternate CA
1693 <li>FontChooser message dialog appears to hang after
1694 choosing 1pt font</li>
1695 <li>Peptide secondary structure incorrectly imported from
1696 annotation file when annotation display text includes 'e' or
1698 <li>Cannot set colour of new feature type whilst creating
1700 <li>cDNA translation alignment should not be sequence
1701 order dependent</li>
1702 <li>'Show unconserved' doesn't work for lower case
1704 <li>Nucleotide ambiguity codes involving R not recognised</li>
1705 </ul> <em>Deployment and Documentation</em>
1707 <li>Applet example pages appear different to the rest of
1708 www.jalview.org</li>
1709 </ul> <em>Application Known issues</em>
1711 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1712 <li>Misleading message appears after trying to delete
1714 <li>Jalview icon not shown in dock after InstallAnywhere
1715 version launches</li>
1716 <li>Fetching EMBL reference for an RNA sequence results
1717 fails with a sequence mismatch</li>
1718 <li>Corrupted or unreadable alignment display when
1719 scrolling alignment to right</li>
1720 <li>ArrayIndexOutOfBoundsException thrown when remove
1721 empty columns called on alignment with ragged gapped ends</li>
1722 <li>auto calculated alignment annotation rows do not get
1723 placed above or below non-autocalculated rows</li>
1724 <li>Jalview dekstop becomes sluggish at full screen in
1725 ultra-high resolution</li>
1726 <li>Cannot disable consensus calculation independently of
1727 quality and conservation</li>
1728 <li>Mouseover highlighting between cDNA and protein can
1729 become sluggish with more than one splitframe shown</li>
1730 </ul> <em>Applet Known Issues</em>
1732 <li>Core PDB parsing code requires Jmol</li>
1733 <li>Sequence canvas panel goes white when alignment
1734 window is being resized</li>
1740 <td><div align="center">
1741 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1743 <td><em>General</em>
1745 <li>Updated Java code signing certificate donated by
1747 <li>Features and annotation preserved when performing
1748 pairwise alignment</li>
1749 <li>RNA pseudoknot annotation can be
1750 imported/exported/displayed</li>
1751 <li>'colour by annotation' can colour by RNA and
1752 protein secondary structure</li>
1753 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1754 post-hoc with 2.9 release</em>)
1757 </ul> <em>Application</em>
1759 <li>Extract and display secondary structure for sequences
1760 with 3D structures</li>
1761 <li>Support for parsing RNAML</li>
1762 <li>Annotations menu for layout
1764 <li>sort sequence annotation rows by alignment</li>
1765 <li>place sequence annotation above/below alignment
1768 <li>Output in Stockholm format</li>
1769 <li>Internationalisation: improved Spanish (es)
1771 <li>Structure viewer preferences tab</li>
1772 <li>Disorder and Secondary Structure annotation tracks
1773 shared between alignments</li>
1774 <li>UCSF Chimera launch and linked highlighting from
1776 <li>Show/hide all sequence associated annotation rows for
1777 all or current selection</li>
1778 <li>disorder and secondary structure predictions
1779 available as dataset annotation</li>
1780 <li>Per-sequence rna helices colouring</li>
1783 <li>Sequence database accessions imported when fetching
1784 alignments from Rfam</li>
1785 <li>update VARNA version to 3.91</li>
1787 <li>New groovy scripts for exporting aligned positions,
1788 conservation values, and calculating sum of pairs scores.</li>
1789 <li>Command line argument to set default JABAWS server</li>
1790 <li>include installation type in build properties and
1791 console log output</li>
1792 <li>Updated Jalview project format to preserve dataset
1796 <!-- issues resolved --> <em>Application</em>
1798 <li>Distinguish alignment and sequence associated RNA
1799 structure in structure->view->VARNA</li>
1800 <li>Raise dialog box if user deletes all sequences in an
1802 <li>Pressing F1 results in documentation opening twice</li>
1803 <li>Sequence feature tooltip is wrapped</li>
1804 <li>Double click on sequence associated annotation
1805 selects only first column</li>
1806 <li>Redundancy removal doesn't result in unlinked
1807 leaves shown in tree</li>
1808 <li>Undos after several redundancy removals don't undo
1810 <li>Hide sequence doesn't hide associated annotation</li>
1811 <li>User defined colours dialog box too big to fit on
1812 screen and buttons not visible</li>
1813 <li>author list isn't updated if already written to
1814 Jalview properties</li>
1815 <li>Popup menu won't open after retrieving sequence
1817 <li>File open window for associate PDB doesn't open</li>
1818 <li>Left-then-right click on a sequence id opens a
1819 browser search window</li>
1820 <li>Cannot open sequence feature shading/sort popup menu
1821 in feature settings dialog</li>
1822 <li>better tooltip placement for some areas of Jalview
1824 <li>Allow addition of JABAWS Server which doesn't
1825 pass validation</li>
1826 <li>Web services parameters dialog box is too large to
1828 <li>Muscle nucleotide alignment preset obscured by
1830 <li>JABAWS preset submenus don't contain newly
1831 defined user preset</li>
1832 <li>MSA web services warns user if they were launched
1833 with invalid input</li>
1834 <li>Jalview cannot contact DAS Registy when running on
1837 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1838 'Superpose with' submenu not shown when new view
1842 </ul> <!-- <em>Applet</em>
1844 </ul> <em>General</em>
1846 </ul>--> <em>Deployment and Documentation</em>
1848 <li>2G and 1G options in launchApp have no effect on
1849 memory allocation</li>
1850 <li>launchApp service doesn't automatically open
1851 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1853 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1854 InstallAnywhere reports cannot find valid JVM when Java
1855 1.7_055 is available
1857 </ul> <em>Application Known issues</em>
1860 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1861 corrupted or unreadable alignment display when scrolling
1865 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1866 retrieval fails but progress bar continues for DAS retrieval
1867 with large number of ID
1870 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1871 flatfile output of visible region has incorrect sequence
1875 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1876 rna structure consensus doesn't update when secondary
1877 structure tracks are rearranged
1880 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1881 invalid rna structure positional highlighting does not
1882 highlight position of invalid base pairs
1885 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1886 out of memory errors are not raised when saving Jalview
1887 project from alignment window file menu
1890 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1891 Switching to RNA Helices colouring doesn't propagate to
1895 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1896 colour by RNA Helices not enabled when user created
1897 annotation added to alignment
1900 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1901 Jalview icon not shown on dock in Mountain Lion/Webstart
1903 </ul> <em>Applet Known Issues</em>
1906 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1907 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1910 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1911 Jalview and Jmol example not compatible with IE9
1914 <li>Sort by annotation score doesn't reverse order
1920 <td><div align="center">
1921 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1924 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1927 <li>Internationalisation of user interface (usually
1928 called i18n support) and translation for Spanish locale</li>
1929 <li>Define/Undefine group on current selection with
1930 Ctrl-G/Shift Ctrl-G</li>
1931 <li>Improved group creation/removal options in
1932 alignment/sequence Popup menu</li>
1933 <li>Sensible precision for symbol distribution
1934 percentages shown in logo tooltip.</li>
1935 <li>Annotation panel height set according to amount of
1936 annotation when alignment first opened</li>
1937 </ul> <em>Application</em>
1939 <li>Interactive consensus RNA secondary structure
1940 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1941 <li>Select columns containing particular features from
1942 Feature Settings dialog</li>
1943 <li>View all 'representative' PDB structures for selected
1945 <li>Update Jalview project format:
1947 <li>New file extension for Jalview projects '.jvp'</li>
1948 <li>Preserve sequence and annotation dataset (to
1949 store secondary structure annotation,etc)</li>
1950 <li>Per group and alignment annotation and RNA helix
1954 <li>New similarity measures for PCA and Tree calculation
1956 <li>Experimental support for retrieval and viewing of
1957 flanking regions for an alignment</li>
1961 <!-- issues resolved --> <em>Application</em>
1963 <li>logo keeps spinning and status remains at queued or
1964 running after job is cancelled</li>
1965 <li>cannot export features from alignments imported from
1966 Jalview/VAMSAS projects</li>
1967 <li>Buggy slider for web service parameters that take
1969 <li>Newly created RNA secondary structure line doesn't
1970 have 'display all symbols' flag set</li>
1971 <li>T-COFFEE alignment score shading scheme and other
1972 annotation shading not saved in Jalview project</li>
1973 <li>Local file cannot be loaded in freshly downloaded
1975 <li>Jalview icon not shown on dock in Mountain
1977 <li>Load file from desktop file browser fails</li>
1978 <li>Occasional NPE thrown when calculating large trees</li>
1979 <li>Cannot reorder or slide sequences after dragging an
1980 alignment onto desktop</li>
1981 <li>Colour by annotation dialog throws NPE after using
1982 'extract scores' function</li>
1983 <li>Loading/cut'n'pasting an empty file leads to a grey
1984 alignment window</li>
1985 <li>Disorder thresholds rendered incorrectly after
1986 performing IUPred disorder prediction</li>
1987 <li>Multiple group annotated consensus rows shown when
1988 changing 'normalise logo' display setting</li>
1989 <li>Find shows blank dialog after 'finished searching' if
1990 nothing matches query</li>
1991 <li>Null Pointer Exceptions raised when sorting by
1992 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1994 <li>Errors in Jmol console when structures in alignment
1995 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1997 <li>Not all working JABAWS services are shown in
1999 <li>JAVAWS version of Jalview fails to launch with
2000 'invalid literal/length code'</li>
2001 <li>Annotation/RNA Helix colourschemes cannot be applied
2002 to alignment with groups (actually fixed in 2.8.0b1)</li>
2003 <li>RNA Helices and T-Coffee Scores available as default
2006 </ul> <em>Applet</em>
2008 <li>Remove group option is shown even when selection is
2010 <li>Apply to all groups ticked but colourscheme changes
2011 don't affect groups</li>
2012 <li>Documented RNA Helices and T-Coffee Scores as valid
2013 colourscheme name</li>
2014 <li>Annotation labels drawn on sequence IDs when
2015 Annotation panel is not displayed</li>
2016 <li>Increased font size for dropdown menus on OSX and
2017 embedded windows</li>
2018 </ul> <em>Other</em>
2020 <li>Consensus sequence for alignments/groups with a
2021 single sequence were not calculated</li>
2022 <li>annotation files that contain only groups imported as
2023 annotation and junk sequences</li>
2024 <li>Fasta files with sequences containing '*' incorrectly
2025 recognised as PFAM or BLC</li>
2026 <li>conservation/PID slider apply all groups option
2027 doesn't affect background (2.8.0b1)
2029 <li>redundancy highlighting is erratic at 0% and 100%</li>
2030 <li>Remove gapped columns fails for sequences with ragged
2032 <li>AMSA annotation row with leading spaces is not
2033 registered correctly on import</li>
2034 <li>Jalview crashes when selecting PCA analysis for
2035 certain alignments</li>
2036 <li>Opening the colour by annotation dialog for an
2037 existing annotation based 'use original colours'
2038 colourscheme loses original colours setting</li>
2043 <td><div align="center">
2044 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2045 <em>30/1/2014</em></strong>
2049 <li>Trusted certificates for JalviewLite applet and
2050 Jalview Desktop application<br />Certificate was donated by
2051 <a href="https://www.certum.eu">Certum</a> to the Jalview
2052 open source project).
2054 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2055 <li>Output in Stockholm format</li>
2056 <li>Allow import of data from gzipped files</li>
2057 <li>Export/import group and sequence associated line
2058 graph thresholds</li>
2059 <li>Nucleotide substitution matrix that supports RNA and
2060 ambiguity codes</li>
2061 <li>Allow disorder predictions to be made on the current
2062 selection (or visible selection) in the same way that JPred
2064 <li>Groovy scripting for headless Jalview operation</li>
2065 </ul> <em>Other improvements</em>
2067 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2068 <li>COMBINE statement uses current SEQUENCE_REF and
2069 GROUP_REF scope to group annotation rows</li>
2070 <li>Support '' style escaping of quotes in Newick
2072 <li>Group options for JABAWS service by command line name</li>
2073 <li>Empty tooltip shown for JABA service options with a
2074 link but no description</li>
2075 <li>Select primary source when selecting authority in
2076 database fetcher GUI</li>
2077 <li>Add .mfa to FASTA file extensions recognised by
2079 <li>Annotation label tooltip text wrap</li>
2084 <li>Slow scrolling when lots of annotation rows are
2086 <li>Lots of NPE (and slowness) after creating RNA
2087 secondary structure annotation line</li>
2088 <li>Sequence database accessions not imported when
2089 fetching alignments from Rfam</li>
2090 <li>Incorrect SHMR submission for sequences with
2092 <li>View all structures does not always superpose
2094 <li>Option widgets in service parameters not updated to
2095 reflect user or preset settings</li>
2096 <li>Null pointer exceptions for some services without
2097 presets or adjustable parameters</li>
2098 <li>Discover PDB IDs entry in structure menu doesn't
2099 discover PDB xRefs</li>
2100 <li>Exception encountered while trying to retrieve
2101 features with DAS</li>
2102 <li>Lowest value in annotation row isn't coloured
2103 when colour by annotation (per sequence) is coloured</li>
2104 <li>Keyboard mode P jumps to start of gapped region when
2105 residue follows a gap</li>
2106 <li>Jalview appears to hang importing an alignment with
2107 Wrap as default or after enabling Wrap</li>
2108 <li>'Right click to add annotations' message
2109 shown in wrap mode when no annotations present</li>
2110 <li>Disorder predictions fail with NPE if no automatic
2111 annotation already exists on alignment</li>
2112 <li>oninit javascript function should be called after
2113 initialisation completes</li>
2114 <li>Remove redundancy after disorder prediction corrupts
2115 alignment window display</li>
2116 <li>Example annotation file in documentation is invalid</li>
2117 <li>Grouped line graph annotation rows are not exported
2118 to annotation file</li>
2119 <li>Multi-harmony analysis cannot be run when only two
2121 <li>Cannot create multiple groups of line graphs with
2122 several 'combine' statements in annotation file</li>
2123 <li>Pressing return several times causes Number Format
2124 exceptions in keyboard mode</li>
2125 <li>Multi-harmony (SHMMR) method doesn't submit
2126 correct partitions for input data</li>
2127 <li>Translation from DNA to Amino Acids fails</li>
2128 <li>Jalview fail to load newick tree with quoted label</li>
2129 <li>--headless flag isn't understood</li>
2130 <li>ClassCastException when generating EPS in headless
2132 <li>Adjusting sequence-associated shading threshold only
2133 changes one row's threshold</li>
2134 <li>Preferences and Feature settings panel panel
2135 doesn't open</li>
2136 <li>hide consensus histogram also hides conservation and
2137 quality histograms</li>
2142 <td><div align="center">
2143 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2145 <td><em>Application</em>
2147 <li>Support for JABAWS 2.0 Services (AACon alignment
2148 conservation, protein disorder and Clustal Omega)</li>
2149 <li>JABAWS server status indicator in Web Services
2151 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2152 in Jalview alignment window</li>
2153 <li>Updated Jalview build and deploy framework for OSX
2154 mountain lion, windows 7, and 8</li>
2155 <li>Nucleotide substitution matrix for PCA that supports
2156 RNA and ambiguity codes</li>
2158 <li>Improved sequence database retrieval GUI</li>
2159 <li>Support fetching and database reference look up
2160 against multiple DAS sources (Fetch all from in 'fetch db
2162 <li>Jalview project improvements
2164 <li>Store and retrieve the 'belowAlignment'
2165 flag for annotation</li>
2166 <li>calcId attribute to group annotation rows on the
2168 <li>Store AACon calculation settings for a view in
2169 Jalview project</li>
2173 <li>horizontal scrolling gesture support</li>
2174 <li>Visual progress indicator when PCA calculation is
2176 <li>Simpler JABA web services menus</li>
2177 <li>visual indication that web service results are still
2178 being retrieved from server</li>
2179 <li>Serialise the dialogs that are shown when Jalview
2180 starts up for first time</li>
2181 <li>Jalview user agent string for interacting with HTTP
2183 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2185 <li>Examples directory and Groovy library included in
2186 InstallAnywhere distribution</li>
2187 </ul> <em>Applet</em>
2189 <li>RNA alignment and secondary structure annotation
2190 visualization applet example</li>
2191 </ul> <em>General</em>
2193 <li>Normalise option for consensus sequence logo</li>
2194 <li>Reset button in PCA window to return dimensions to
2196 <li>Allow seqspace or Jalview variant of alignment PCA
2198 <li>PCA with either nucleic acid and protein substitution
2200 <li>Allow windows containing HTML reports to be exported
2202 <li>Interactive display and editing of RNA secondary
2203 structure contacts</li>
2204 <li>RNA Helix Alignment Colouring</li>
2205 <li>RNA base pair logo consensus</li>
2206 <li>Parse sequence associated secondary structure
2207 information in Stockholm files</li>
2208 <li>HTML Export database accessions and annotation
2209 information presented in tooltip for sequences</li>
2210 <li>Import secondary structure from LOCARNA clustalw
2211 style RNA alignment files</li>
2212 <li>import and visualise T-COFFEE quality scores for an
2214 <li>'colour by annotation' per sequence option to
2215 shade each sequence according to its associated alignment
2217 <li>New Jalview Logo</li>
2218 </ul> <em>Documentation and Development</em>
2220 <li>documentation for score matrices used in Jalview</li>
2221 <li>New Website!</li>
2223 <td><em>Application</em>
2225 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2226 wsdbfetch REST service</li>
2227 <li>Stop windows being moved outside desktop on OSX</li>
2228 <li>Filetype associations not installed for webstart
2230 <li>Jalview does not always retrieve progress of a JABAWS
2231 job execution in full once it is complete</li>
2232 <li>revise SHMR RSBS definition to ensure alignment is
2233 uploaded via ali_file parameter</li>
2234 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2235 <li>View all structures superposed fails with exception</li>
2236 <li>Jnet job queues forever if a very short sequence is
2237 submitted for prediction</li>
2238 <li>Cut and paste menu not opened when mouse clicked on
2240 <li>Putting fractional value into integer text box in
2241 alignment parameter dialog causes Jalview to hang</li>
2242 <li>Structure view highlighting doesn't work on
2244 <li>View all structures fails with exception shown in
2246 <li>Characters in filename associated with PDBEntry not
2247 escaped in a platform independent way</li>
2248 <li>Jalview desktop fails to launch with exception when
2250 <li>Tree calculation reports 'you must have 2 or more
2251 sequences selected' when selection is empty</li>
2252 <li>Jalview desktop fails to launch with jar signature
2253 failure when java web start temporary file caching is
2255 <li>DAS Sequence retrieval with range qualification
2256 results in sequence xref which includes range qualification</li>
2257 <li>Errors during processing of command line arguments
2258 cause progress bar (JAL-898) to be removed</li>
2259 <li>Replace comma for semi-colon option not disabled for
2260 DAS sources in sequence fetcher</li>
2261 <li>Cannot close news reader when JABAWS server warning
2262 dialog is shown</li>
2263 <li>Option widgets not updated to reflect user settings</li>
2264 <li>Edited sequence not submitted to web service</li>
2265 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2266 <li>InstallAnywhere installer doesn't unpack and run
2267 on OSX Mountain Lion</li>
2268 <li>Annotation panel not given a scroll bar when
2269 sequences with alignment annotation are pasted into the
2271 <li>Sequence associated annotation rows not associated
2272 when loaded from Jalview project</li>
2273 <li>Browser launch fails with NPE on java 1.7</li>
2274 <li>JABAWS alignment marked as finished when job was
2275 cancelled or job failed due to invalid input</li>
2276 <li>NPE with v2.7 example when clicking on Tree
2277 associated with all views</li>
2278 <li>Exceptions when copy/paste sequences with grouped
2279 annotation rows to new window</li>
2280 </ul> <em>Applet</em>
2282 <li>Sequence features are momentarily displayed before
2283 they are hidden using hidefeaturegroups applet parameter</li>
2284 <li>loading features via javascript API automatically
2285 enables feature display</li>
2286 <li>scrollToColumnIn javascript API method doesn't
2288 </ul> <em>General</em>
2290 <li>Redundancy removal fails for rna alignment</li>
2291 <li>PCA calculation fails when sequence has been selected
2292 and then deselected</li>
2293 <li>PCA window shows grey box when first opened on OSX</li>
2294 <li>Letters coloured pink in sequence logo when alignment
2295 coloured with clustalx</li>
2296 <li>Choosing fonts without letter symbols defined causes
2297 exceptions and redraw errors</li>
2298 <li>Initial PCA plot view is not same as manually
2299 reconfigured view</li>
2300 <li>Grouped annotation graph label has incorrect line
2302 <li>Grouped annotation graph label display is corrupted
2303 for lots of labels</li>
2308 <div align="center">
2309 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2312 <td><em>Application</em>
2314 <li>Jalview Desktop News Reader</li>
2315 <li>Tweaked default layout of web services menu</li>
2316 <li>View/alignment association menu to enable user to
2317 easily specify which alignment a multi-structure view takes
2318 its colours/correspondences from</li>
2319 <li>Allow properties file location to be specified as URL</li>
2320 <li>Extend Jalview project to preserve associations
2321 between many alignment views and a single Jmol display</li>
2322 <li>Store annotation row height in Jalview project file</li>
2323 <li>Annotation row column label formatting attributes
2324 stored in project file</li>
2325 <li>Annotation row order for auto-calculated annotation
2326 rows preserved in Jalview project file</li>
2327 <li>Visual progress indication when Jalview state is
2328 saved using Desktop window menu</li>
2329 <li>Visual indication that command line arguments are
2330 still being processed</li>
2331 <li>Groovy script execution from URL</li>
2332 <li>Colour by annotation default min and max colours in
2334 <li>Automatically associate PDB files dragged onto an
2335 alignment with sequences that have high similarity and
2337 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2338 <li>'view structures' option to open many
2339 structures in same window</li>
2340 <li>Sort associated views menu option for tree panel</li>
2341 <li>Group all JABA and non-JABA services for a particular
2342 analysis function in its own submenu</li>
2343 </ul> <em>Applet</em>
2345 <li>Userdefined and autogenerated annotation rows for
2347 <li>Adjustment of alignment annotation pane height</li>
2348 <li>Annotation scrollbar for annotation panel</li>
2349 <li>Drag to reorder annotation rows in annotation panel</li>
2350 <li>'automaticScrolling' parameter</li>
2351 <li>Allow sequences with partial ID string matches to be
2352 annotated from GFF/Jalview features files</li>
2353 <li>Sequence logo annotation row in applet</li>
2354 <li>Absolute paths relative to host server in applet
2355 parameters are treated as such</li>
2356 <li>New in the JalviewLite javascript API:
2358 <li>JalviewLite.js javascript library</li>
2359 <li>Javascript callbacks for
2361 <li>Applet initialisation</li>
2362 <li>Sequence/alignment mouse-overs and selections</li>
2365 <li>scrollTo row and column alignment scrolling
2367 <li>Select sequence/alignment regions from javascript</li>
2368 <li>javascript structure viewer harness to pass
2369 messages between Jmol and Jalview when running as
2370 distinct applets</li>
2371 <li>sortBy method</li>
2372 <li>Set of applet and application examples shipped
2373 with documentation</li>
2374 <li>New example to demonstrate JalviewLite and Jmol
2375 javascript message exchange</li>
2377 </ul> <em>General</em>
2379 <li>Enable Jmol displays to be associated with multiple
2380 multiple alignments</li>
2381 <li>Option to automatically sort alignment with new tree</li>
2382 <li>User configurable link to enable redirects to a
2383 www.Jalview.org mirror</li>
2384 <li>Jmol colours option for Jmol displays</li>
2385 <li>Configurable newline string when writing alignment
2386 and other flat files</li>
2387 <li>Allow alignment annotation description lines to
2388 contain html tags</li>
2389 </ul> <em>Documentation and Development</em>
2391 <li>Add groovy test harness for bulk load testing to
2393 <li>Groovy script to load and align a set of sequences
2394 using a web service before displaying the result in the
2395 Jalview desktop</li>
2396 <li>Restructured javascript and applet api documentation</li>
2397 <li>Ant target to publish example html files with applet
2399 <li>Netbeans project for building Jalview from source</li>
2400 <li>ant task to create online javadoc for Jalview source</li>
2402 <td><em>Application</em>
2404 <li>User defined colourscheme throws exception when
2405 current built in colourscheme is saved as new scheme</li>
2406 <li>AlignFrame->Save in application pops up save
2407 dialog for valid filename/format</li>
2408 <li>Cannot view associated structure for UniProt sequence</li>
2409 <li>PDB file association breaks for UniProt sequence
2411 <li>Associate PDB from file dialog does not tell you
2412 which sequence is to be associated with the file</li>
2413 <li>Find All raises null pointer exception when query
2414 only matches sequence IDs</li>
2415 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2416 <li>Jalview project with Jmol views created with Jalview
2417 2.4 cannot be loaded</li>
2418 <li>Filetype associations not installed for webstart
2420 <li>Two or more chains in a single PDB file associated
2421 with sequences in different alignments do not get coloured
2422 by their associated sequence</li>
2423 <li>Visibility status of autocalculated annotation row
2424 not preserved when project is loaded</li>
2425 <li>Annotation row height and visibility attributes not
2426 stored in Jalview project</li>
2427 <li>Tree bootstraps are not preserved when saved as a
2428 Jalview project</li>
2429 <li>Envision2 workflow tooltips are corrupted</li>
2430 <li>Enabling show group conservation also enables colour
2431 by conservation</li>
2432 <li>Duplicate group associated conservation or consensus
2433 created on new view</li>
2434 <li>Annotation scrollbar not displayed after 'show
2435 all hidden annotation rows' option selected</li>
2436 <li>Alignment quality not updated after alignment
2437 annotation row is hidden then shown</li>
2438 <li>Preserve colouring of structures coloured by
2439 sequences in pre Jalview 2.7 projects</li>
2440 <li>Web service job parameter dialog is not laid out
2442 <li>Web services menu not refreshed after 'reset
2443 services' button is pressed in preferences</li>
2444 <li>Annotation off by one in Jalview v2_3 example project</li>
2445 <li>Structures imported from file and saved in project
2446 get name like jalview_pdb1234.txt when reloaded</li>
2447 <li>Jalview does not always retrieve progress of a JABAWS
2448 job execution in full once it is complete</li>
2449 </ul> <em>Applet</em>
2451 <li>Alignment height set incorrectly when lots of
2452 annotation rows are displayed</li>
2453 <li>Relative URLs in feature HTML text not resolved to
2455 <li>View follows highlighting does not work for positions
2457 <li><= shown as = in tooltip</li>
2458 <li>Export features raises exception when no features
2460 <li>Separator string used for serialising lists of IDs
2461 for javascript api is modified when separator string
2462 provided as parameter</li>
2463 <li>Null pointer exception when selecting tree leaves for
2464 alignment with no existing selection</li>
2465 <li>Relative URLs for datasources assumed to be relative
2466 to applet's codebase</li>
2467 <li>Status bar not updated after finished searching and
2468 search wraps around to first result</li>
2469 <li>StructureSelectionManager instance shared between
2470 several Jalview applets causes race conditions and memory
2472 <li>Hover tooltip and mouseover of position on structure
2473 not sent from Jmol in applet</li>
2474 <li>Certain sequences of javascript method calls to
2475 applet API fatally hang browser</li>
2476 </ul> <em>General</em>
2478 <li>View follows structure mouseover scrolls beyond
2479 position with wrapped view and hidden regions</li>
2480 <li>Find sequence position moves to wrong residue
2481 with/without hidden columns</li>
2482 <li>Sequence length given in alignment properties window
2484 <li>InvalidNumberFormat exceptions thrown when trying to
2485 import PDB like structure files</li>
2486 <li>Positional search results are only highlighted
2487 between user-supplied sequence start/end bounds</li>
2488 <li>End attribute of sequence is not validated</li>
2489 <li>Find dialog only finds first sequence containing a
2490 given sequence position</li>
2491 <li>Sequence numbering not preserved in MSF alignment
2493 <li>Jalview PDB file reader does not extract sequence
2494 from nucleotide chains correctly</li>
2495 <li>Structure colours not updated when tree partition
2496 changed in alignment</li>
2497 <li>Sequence associated secondary structure not correctly
2498 parsed in interleaved stockholm</li>
2499 <li>Colour by annotation dialog does not restore current
2501 <li>Hiding (nearly) all sequences doesn't work
2503 <li>Sequences containing lowercase letters are not
2504 properly associated with their pdb files</li>
2505 </ul> <em>Documentation and Development</em>
2507 <li>schemas/JalviewWsParamSet.xsd corrupted by
2508 ApplyCopyright tool</li>
2513 <div align="center">
2514 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2517 <td><em>Application</em>
2519 <li>New warning dialog when the Jalview Desktop cannot
2520 contact web services</li>
2521 <li>JABA service parameters for a preset are shown in
2522 service job window</li>
2523 <li>JABA Service menu entries reworded</li>
2527 <li>Modeller PIR IO broken - cannot correctly import a
2528 pir file emitted by Jalview</li>
2529 <li>Existing feature settings transferred to new
2530 alignment view created from cut'n'paste</li>
2531 <li>Improved test for mixed amino/nucleotide chains when
2532 parsing PDB files</li>
2533 <li>Consensus and conservation annotation rows
2534 occasionally become blank for all new windows</li>
2535 <li>Exception raised when right clicking above sequences
2536 in wrapped view mode</li>
2537 </ul> <em>Application</em>
2539 <li>multiple multiply aligned structure views cause cpu
2540 usage to hit 100% and computer to hang</li>
2541 <li>Web Service parameter layout breaks for long user
2542 parameter names</li>
2543 <li>Jaba service discovery hangs desktop if Jaba server
2550 <div align="center">
2551 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2554 <td><em>Application</em>
2556 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2557 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2560 <li>Web Services preference tab</li>
2561 <li>Analysis parameters dialog box and user defined
2563 <li>Improved speed and layout of Envision2 service menu</li>
2564 <li>Superpose structures using associated sequence
2566 <li>Export coordinates and projection as CSV from PCA
2568 </ul> <em>Applet</em>
2570 <li>enable javascript: execution by the applet via the
2571 link out mechanism</li>
2572 </ul> <em>Other</em>
2574 <li>Updated the Jmol Jalview interface to work with Jmol
2576 <li>The Jalview Desktop and JalviewLite applet now
2577 require Java 1.5</li>
2578 <li>Allow Jalview feature colour specification for GFF
2579 sequence annotation files</li>
2580 <li>New 'colour by label' keword in Jalview feature file
2581 type colour specification</li>
2582 <li>New Jalview Desktop Groovy API method that allows a
2583 script to check if it being run in an interactive session or
2584 in a batch operation from the Jalview command line</li>
2588 <li>clustalx colourscheme colours Ds preferentially when
2589 both D+E are present in over 50% of the column</li>
2590 </ul> <em>Application</em>
2592 <li>typo in AlignmentFrame->View->Hide->all but
2593 selected Regions menu item</li>
2594 <li>sequence fetcher replaces ',' for ';' when the ',' is
2595 part of a valid accession ID</li>
2596 <li>fatal OOM if object retrieved by sequence fetcher
2597 runs out of memory</li>
2598 <li>unhandled Out of Memory Error when viewing pca
2599 analysis results</li>
2600 <li>InstallAnywhere builds fail to launch on OS X java
2601 10.5 update 4 (due to apple Java 1.6 update)</li>
2602 <li>Installanywhere Jalview silently fails to launch</li>
2603 </ul> <em>Applet</em>
2605 <li>Jalview.getFeatureGroups() raises an
2606 ArrayIndexOutOfBoundsException if no feature groups are
2613 <div align="center">
2614 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2620 <li>Alignment prettyprinter doesn't cope with long
2622 <li>clustalx colourscheme colours Ds preferentially when
2623 both D+E are present in over 50% of the column</li>
2624 <li>nucleic acid structures retrieved from PDB do not
2625 import correctly</li>
2626 <li>More columns get selected than were clicked on when a
2627 number of columns are hidden</li>
2628 <li>annotation label popup menu not providing correct
2629 add/hide/show options when rows are hidden or none are
2631 <li>Stockholm format shown in list of readable formats,
2632 and parser copes better with alignments from RFAM.</li>
2633 <li>CSV output of consensus only includes the percentage
2634 of all symbols if sequence logo display is enabled</li>
2636 </ul> <em>Applet</em>
2638 <li>annotation panel disappears when annotation is
2640 </ul> <em>Application</em>
2642 <li>Alignment view not redrawn properly when new
2643 alignment opened where annotation panel is visible but no
2644 annotations are present on alignment</li>
2645 <li>pasted region containing hidden columns is
2646 incorrectly displayed in new alignment window</li>
2647 <li>Jalview slow to complete operations when stdout is
2648 flooded (fix is to close the Jalview console)</li>
2649 <li>typo in AlignmentFrame->View->Hide->all but
2650 selected Rregions menu item.</li>
2651 <li>inconsistent group submenu and Format submenu entry
2652 'Un' or 'Non'conserved</li>
2653 <li>Sequence feature settings are being shared by
2654 multiple distinct alignments</li>
2655 <li>group annotation not recreated when tree partition is
2657 <li>double click on group annotation to select sequences
2658 does not propagate to associated trees</li>
2659 <li>Mac OSX specific issues:
2661 <li>exception raised when mouse clicked on desktop
2662 window background</li>
2663 <li>Desktop menu placed on menu bar and application
2664 name set correctly</li>
2665 <li>sequence feature settings not wide enough for the
2666 save feature colourscheme button</li>
2675 <div align="center">
2676 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2679 <td><em>New Capabilities</em>
2681 <li>URL links generated from description line for
2682 regular-expression based URL links (applet and application)
2684 <li>Non-positional feature URL links are shown in link
2686 <li>Linked viewing of nucleic acid sequences and
2688 <li>Automatic Scrolling option in View menu to display
2689 the currently highlighted region of an alignment.</li>
2690 <li>Order an alignment by sequence length, or using the
2691 average score or total feature count for each sequence.</li>
2692 <li>Shading features by score or associated description</li>
2693 <li>Subdivide alignment and groups based on identity of
2694 selected subsequence (Make Groups from Selection).</li>
2695 <li>New hide/show options including Shift+Control+H to
2696 hide everything but the currently selected region.</li>
2697 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2698 </ul> <em>Application</em>
2700 <li>Fetch DB References capabilities and UI expanded to
2701 support retrieval from DAS sequence sources</li>
2702 <li>Local DAS Sequence sources can be added via the
2703 command line or via the Add local source dialog box.</li>
2704 <li>DAS Dbref and DbxRef feature types are parsed as
2705 database references and protein_name is parsed as
2706 description line (BioSapiens terms).</li>
2707 <li>Enable or disable non-positional feature and database
2708 references in sequence ID tooltip from View menu in
2710 <!-- <li>New hidden columns and rows and representatives capabilities
2711 in annotations file (in progress - not yet fully implemented)</li> -->
2712 <li>Group-associated consensus, sequence logos and
2713 conservation plots</li>
2714 <li>Symbol distributions for each column can be exported
2715 and visualized as sequence logos</li>
2716 <li>Optionally scale multi-character column labels to fit
2717 within each column of annotation row<!-- todo for applet -->
2719 <li>Optional automatic sort of associated alignment view
2720 when a new tree is opened.</li>
2721 <li>Jalview Java Console</li>
2722 <li>Better placement of desktop window when moving
2723 between different screens.</li>
2724 <li>New preference items for sequence ID tooltip and
2725 consensus annotation</li>
2726 <li>Client to submit sequences and IDs to Envision2
2728 <li><em>Vamsas Capabilities</em>
2730 <li>Improved VAMSAS synchronization (Jalview archive
2731 used to preserve views, structures, and tree display
2733 <li>Import of vamsas documents from disk or URL via
2735 <li>Sharing of selected regions between views and
2736 with other VAMSAS applications (Experimental feature!)</li>
2737 <li>Updated API to VAMSAS version 0.2</li>
2739 </ul> <em>Applet</em>
2741 <li>Middle button resizes annotation row height</li>
2744 <li>sortByTree (true/false) - automatically sort the
2745 associated alignment view by the tree when a new tree is
2747 <li>showTreeBootstraps (true/false) - show or hide
2748 branch bootstraps (default is to show them if available)</li>
2749 <li>showTreeDistances (true/false) - show or hide
2750 branch lengths (default is to show them if available)</li>
2751 <li>showUnlinkedTreeNodes (true/false) - indicate if
2752 unassociated nodes should be highlighted in the tree
2754 <li>heightScale and widthScale (1.0 or more) -
2755 increase the height or width of a cell in the alignment
2756 grid relative to the current font size.</li>
2759 <li>Non-positional features displayed in sequence ID
2761 </ul> <em>Other</em>
2763 <li>Features format: graduated colour definitions and
2764 specification of feature scores</li>
2765 <li>Alignment Annotations format: new keywords for group
2766 associated annotation (GROUP_REF) and annotation row display
2767 properties (ROW_PROPERTIES)</li>
2768 <li>XML formats extended to support graduated feature
2769 colourschemes, group associated annotation, and profile
2770 visualization settings.</li></td>
2773 <li>Source field in GFF files parsed as feature source
2774 rather than description</li>
2775 <li>Non-positional features are now included in sequence
2776 feature and gff files (controlled via non-positional feature
2777 visibility in tooltip).</li>
2778 <li>URL links generated for all feature links (bugfix)</li>
2779 <li>Added URL embedding instructions to features file
2781 <li>Codons containing ambiguous nucleotides translated as
2782 'X' in peptide product</li>
2783 <li>Match case switch in find dialog box works for both
2784 sequence ID and sequence string and query strings do not
2785 have to be in upper case to match case-insensitively.</li>
2786 <li>AMSA files only contain first column of
2787 multi-character column annotation labels</li>
2788 <li>Jalview Annotation File generation/parsing consistent
2789 with documentation (e.g. Stockholm annotation can be
2790 exported and re-imported)</li>
2791 <li>PDB files without embedded PDB IDs given a friendly
2793 <li>Find incrementally searches ID string matches as well
2794 as subsequence matches, and correctly reports total number
2798 <li>Better handling of exceptions during sequence
2800 <li>Dasobert generated non-positional feature URL
2801 link text excludes the start_end suffix</li>
2802 <li>DAS feature and source retrieval buttons disabled
2803 when fetch or registry operations in progress.</li>
2804 <li>PDB files retrieved from URLs are cached properly</li>
2805 <li>Sequence description lines properly shared via
2807 <li>Sequence fetcher fetches multiple records for all
2809 <li>Ensured that command line das feature retrieval
2810 completes before alignment figures are generated.</li>
2811 <li>Reduced time taken when opening file browser for
2813 <li>isAligned check prior to calculating tree, PCA or
2814 submitting an MSA to JNet now excludes hidden sequences.</li>
2815 <li>User defined group colours properly recovered
2816 from Jalview projects.</li>
2825 <div align="center">
2826 <strong>2.4.0.b2</strong><br> 28/10/2009
2831 <li>Experimental support for google analytics usage
2833 <li>Jalview privacy settings (user preferences and docs).</li>
2838 <li>Race condition in applet preventing startup in
2840 <li>Exception when feature created from selection beyond
2841 length of sequence.</li>
2842 <li>Allow synthetic PDB files to be imported gracefully</li>
2843 <li>Sequence associated annotation rows associate with
2844 all sequences with a given id</li>
2845 <li>Find function matches case-insensitively for sequence
2846 ID string searches</li>
2847 <li>Non-standard characters do not cause pairwise
2848 alignment to fail with exception</li>
2849 </ul> <em>Application Issues</em>
2851 <li>Sequences are now validated against EMBL database</li>
2852 <li>Sequence fetcher fetches multiple records for all
2854 </ul> <em>InstallAnywhere Issues</em>
2856 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2857 issue with installAnywhere mechanism)</li>
2858 <li>Command line launching of JARs from InstallAnywhere
2859 version (java class versioning error fixed)</li>
2866 <div align="center">
2867 <strong>2.4</strong><br> 27/8/2008
2870 <td><em>User Interface</em>
2872 <li>Linked highlighting of codon and amino acid from
2873 translation and protein products</li>
2874 <li>Linked highlighting of structure associated with
2875 residue mapping to codon position</li>
2876 <li>Sequence Fetcher provides example accession numbers
2877 and 'clear' button</li>
2878 <li>MemoryMonitor added as an option under Desktop's
2880 <li>Extract score function to parse whitespace separated
2881 numeric data in description line</li>
2882 <li>Column labels in alignment annotation can be centred.</li>
2883 <li>Tooltip for sequence associated annotation give name
2885 </ul> <em>Web Services and URL fetching</em>
2887 <li>JPred3 web service</li>
2888 <li>Prototype sequence search client (no public services
2890 <li>Fetch either seed alignment or full alignment from
2892 <li>URL Links created for matching database cross
2893 references as well as sequence ID</li>
2894 <li>URL Links can be created using regular-expressions</li>
2895 </ul> <em>Sequence Database Connectivity</em>
2897 <li>Retrieval of cross-referenced sequences from other
2899 <li>Generalised database reference retrieval and
2900 validation to all fetchable databases</li>
2901 <li>Fetch sequences from DAS sources supporting the
2902 sequence command</li>
2903 </ul> <em>Import and Export</em>
2904 <li>export annotation rows as CSV for spreadsheet import</li>
2905 <li>Jalview projects record alignment dataset associations,
2906 EMBL products, and cDNA sequence mappings</li>
2907 <li>Sequence Group colour can be specified in Annotation
2909 <li>Ad-hoc colouring of group in Annotation File using RGB
2910 triplet as name of colourscheme</li>
2911 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2913 <li>treenode binding for VAMSAS tree exchange</li>
2914 <li>local editing and update of sequences in VAMSAS
2915 alignments (experimental)</li>
2916 <li>Create new or select existing session to join</li>
2917 <li>load and save of vamsas documents</li>
2918 </ul> <em>Application command line</em>
2920 <li>-tree parameter to open trees (introduced for passing
2922 <li>-fetchfrom command line argument to specify nicknames
2923 of DAS servers to query for alignment features</li>
2924 <li>-dasserver command line argument to add new servers
2925 that are also automatically queried for features</li>
2926 <li>-groovy command line argument executes a given groovy
2927 script after all input data has been loaded and parsed</li>
2928 </ul> <em>Applet-Application data exchange</em>
2930 <li>Trees passed as applet parameters can be passed to
2931 application (when using "View in full
2932 application")</li>
2933 </ul> <em>Applet Parameters</em>
2935 <li>feature group display control parameter</li>
2936 <li>debug parameter</li>
2937 <li>showbutton parameter</li>
2938 </ul> <em>Applet API methods</em>
2940 <li>newView public method</li>
2941 <li>Window (current view) specific get/set public methods</li>
2942 <li>Feature display control methods</li>
2943 <li>get list of currently selected sequences</li>
2944 </ul> <em>New Jalview distribution features</em>
2946 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2947 <li>RELEASE file gives build properties for the latest
2948 Jalview release.</li>
2949 <li>Java 1.1 Applet build made easier and donotobfuscate
2950 property controls execution of obfuscator</li>
2951 <li>Build target for generating source distribution</li>
2952 <li>Debug flag for javacc</li>
2953 <li>.jalview_properties file is documented (slightly) in
2954 jalview.bin.Cache</li>
2955 <li>Continuous Build Integration for stable and
2956 development version of Application, Applet and source
2961 <li>selected region output includes visible annotations
2962 (for certain formats)</li>
2963 <li>edit label/displaychar contains existing label/char
2965 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2966 <li>shorter peptide product names from EMBL records</li>
2967 <li>Newick string generator makes compact representations</li>
2968 <li>bootstrap values parsed correctly for tree files with
2970 <li>pathological filechooser bug avoided by not allowing
2971 filenames containing a ':'</li>
2972 <li>Fixed exception when parsing GFF files containing
2973 global sequence features</li>
2974 <li>Alignment datasets are finalized only when number of
2975 references from alignment sequences goes to zero</li>
2976 <li>Close of tree branch colour box without colour
2977 selection causes cascading exceptions</li>
2978 <li>occasional negative imgwidth exceptions</li>
2979 <li>better reporting of non-fatal warnings to user when
2980 file parsing fails.</li>
2981 <li>Save works when Jalview project is default format</li>
2982 <li>Save as dialog opened if current alignment format is
2983 not a valid output format</li>
2984 <li>UniProt canonical names introduced for both das and
2986 <li>Histidine should be midblue (not pink!) in Zappo</li>
2987 <li>error messages passed up and output when data read
2989 <li>edit undo recovers previous dataset sequence when
2990 sequence is edited</li>
2991 <li>allow PDB files without pdb ID HEADER lines (like
2992 those generated by MODELLER) to be read in properly</li>
2993 <li>allow reading of JPred concise files as a normal
2995 <li>Stockholm annotation parsing and alignment properties
2996 import fixed for PFAM records</li>
2997 <li>Structure view windows have correct name in Desktop
2999 <li>annotation consisting of sequence associated scores
3000 can be read and written correctly to annotation file</li>
3001 <li>Aligned cDNA translation to aligned peptide works
3003 <li>Fixed display of hidden sequence markers and
3004 non-italic font for representatives in Applet</li>
3005 <li>Applet Menus are always embedded in applet window on
3007 <li>Newly shown features appear at top of stack (in
3009 <li>Annotations added via parameter not drawn properly
3010 due to null pointer exceptions</li>
3011 <li>Secondary structure lines are drawn starting from
3012 first column of alignment</li>
3013 <li>UniProt XML import updated for new schema release in
3015 <li>Sequence feature to sequence ID match for Features
3016 file is case-insensitive</li>
3017 <li>Sequence features read from Features file appended to
3018 all sequences with matching IDs</li>
3019 <li>PDB structure coloured correctly for associated views
3020 containing a sub-sequence</li>
3021 <li>PDB files can be retrieved by applet from Jar files</li>
3022 <li>feature and annotation file applet parameters
3023 referring to different directories are retrieved correctly</li>
3024 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3025 <li>Fixed application hang whilst waiting for
3026 splash-screen version check to complete</li>
3027 <li>Applet properly URLencodes input parameter values
3028 when passing them to the launchApp service</li>
3029 <li>display name and local features preserved in results
3030 retrieved from web service</li>
3031 <li>Visual delay indication for sequence retrieval and
3032 sequence fetcher initialisation</li>
3033 <li>updated Application to use DAS 1.53e version of
3034 dasobert DAS client</li>
3035 <li>Re-instated Full AMSA support and .amsa file
3037 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3045 <div align="center">
3046 <strong>2.3</strong><br> 9/5/07
3051 <li>Jmol 11.0.2 integration</li>
3052 <li>PDB views stored in Jalview XML files</li>
3053 <li>Slide sequences</li>
3054 <li>Edit sequence in place</li>
3055 <li>EMBL CDS features</li>
3056 <li>DAS Feature mapping</li>
3057 <li>Feature ordering</li>
3058 <li>Alignment Properties</li>
3059 <li>Annotation Scores</li>
3060 <li>Sort by scores</li>
3061 <li>Feature/annotation editing in applet</li>
3066 <li>Headless state operation in 2.2.1</li>
3067 <li>Incorrect and unstable DNA pairwise alignment</li>
3068 <li>Cut and paste of sequences with annotation</li>
3069 <li>Feature group display state in XML</li>
3070 <li>Feature ordering in XML</li>
3071 <li>blc file iteration selection using filename # suffix</li>
3072 <li>Stockholm alignment properties</li>
3073 <li>Stockhom alignment secondary structure annotation</li>
3074 <li>2.2.1 applet had no feature transparency</li>
3075 <li>Number pad keys can be used in cursor mode</li>
3076 <li>Structure Viewer mirror image resolved</li>
3083 <div align="center">
3084 <strong>2.2.1</strong><br> 12/2/07
3089 <li>Non standard characters can be read and displayed
3090 <li>Annotations/Features can be imported/exported to the
3092 <li>Applet allows editing of sequence/annotation/group
3093 name & description
3094 <li>Preference setting to display sequence name in
3096 <li>Annotation file format extended to allow
3097 Sequence_groups to be defined
3098 <li>Default opening of alignment overview panel can be
3099 specified in preferences
3100 <li>PDB residue numbering annotation added to associated
3106 <li>Applet crash under certain Linux OS with Java 1.6
3108 <li>Annotation file export / import bugs fixed
3109 <li>PNG / EPS image output bugs fixed
3115 <div align="center">
3116 <strong>2.2</strong><br> 27/11/06
3121 <li>Multiple views on alignment
3122 <li>Sequence feature editing
3123 <li>"Reload" alignment
3124 <li>"Save" to current filename
3125 <li>Background dependent text colour
3126 <li>Right align sequence ids
3127 <li>User-defined lower case residue colours
3130 <li>Menu item accelerator keys
3131 <li>Control-V pastes to current alignment
3132 <li>Cancel button for DAS Feature Fetching
3133 <li>PCA and PDB Viewers zoom via mouse roller
3134 <li>User-defined sub-tree colours and sub-tree selection
3136 <li>'New Window' button on the 'Output to Text box'
3141 <li>New memory efficient Undo/Redo System
3142 <li>Optimised symbol lookups and conservation/consensus
3144 <li>Region Conservation/Consensus recalculated after
3146 <li>Fixed Remove Empty Columns Bug (empty columns at end
3148 <li>Slowed DAS Feature Fetching for increased robustness.
3150 <li>Made angle brackets in ASCII feature descriptions
3152 <li>Re-instated Zoom function for PCA
3153 <li>Sequence descriptions conserved in web service
3155 <li>UniProt ID discoverer uses any word separated by
3157 <li>WsDbFetch query/result association resolved
3158 <li>Tree leaf to sequence mapping improved
3159 <li>Smooth fonts switch moved to FontChooser dialog box.
3166 <div align="center">
3167 <strong>2.1.1</strong><br> 12/9/06
3172 <li>Copy consensus sequence to clipboard</li>
3177 <li>Image output - rightmost residues are rendered if
3178 sequence id panel has been resized</li>
3179 <li>Image output - all offscreen group boundaries are
3181 <li>Annotation files with sequence references - all
3182 elements in file are relative to sequence position</li>
3183 <li>Mac Applet users can use Alt key for group editing</li>
3189 <div align="center">
3190 <strong>2.1</strong><br> 22/8/06
3195 <li>MAFFT Multiple Alignment in default Web Service list</li>
3196 <li>DAS Feature fetching</li>
3197 <li>Hide sequences and columns</li>
3198 <li>Export Annotations and Features</li>
3199 <li>GFF file reading / writing</li>
3200 <li>Associate structures with sequences from local PDB
3202 <li>Add sequences to exisiting alignment</li>
3203 <li>Recently opened files / URL lists</li>
3204 <li>Applet can launch the full application</li>
3205 <li>Applet has transparency for features (Java 1.2
3207 <li>Applet has user defined colours parameter</li>
3208 <li>Applet can load sequences from parameter
3209 "sequence<em>x</em>"
3215 <li>Redundancy Panel reinstalled in the Applet</li>
3216 <li>Monospaced font - EPS / rescaling bug fixed</li>
3217 <li>Annotation files with sequence references bug fixed</li>
3223 <div align="center">
3224 <strong>2.08.1</strong><br> 2/5/06
3229 <li>Change case of selected region from Popup menu</li>
3230 <li>Choose to match case when searching</li>
3231 <li>Middle mouse button and mouse movement can compress /
3232 expand the visible width and height of the alignment</li>
3237 <li>Annotation Panel displays complete JNet results</li>
3243 <div align="center">
3244 <strong>2.08b</strong><br> 18/4/06
3250 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3251 <li>Righthand label on wrapped alignments shows correct
3258 <div align="center">
3259 <strong>2.08</strong><br> 10/4/06
3264 <li>Editing can be locked to the selection area</li>
3265 <li>Keyboard editing</li>
3266 <li>Create sequence features from searches</li>
3267 <li>Precalculated annotations can be loaded onto
3269 <li>Features file allows grouping of features</li>
3270 <li>Annotation Colouring scheme added</li>
3271 <li>Smooth fonts off by default - Faster rendering</li>
3272 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3277 <li>Drag & Drop fixed on Linux</li>
3278 <li>Jalview Archive file faster to load/save, sequence
3279 descriptions saved.</li>
3285 <div align="center">
3286 <strong>2.07</strong><br> 12/12/05
3291 <li>PDB Structure Viewer enhanced</li>
3292 <li>Sequence Feature retrieval and display enhanced</li>
3293 <li>Choose to output sequence start-end after sequence
3294 name for file output</li>
3295 <li>Sequence Fetcher WSDBFetch@EBI</li>
3296 <li>Applet can read feature files, PDB files and can be
3297 used for HTML form input</li>
3302 <li>HTML output writes groups and features</li>
3303 <li>Group editing is Control and mouse click</li>
3304 <li>File IO bugs</li>
3310 <div align="center">
3311 <strong>2.06</strong><br> 28/9/05
3316 <li>View annotations in wrapped mode</li>
3317 <li>More options for PCA viewer</li>
3322 <li>GUI bugs resolved</li>
3323 <li>Runs with -nodisplay from command line</li>
3329 <div align="center">
3330 <strong>2.05b</strong><br> 15/9/05
3335 <li>Choose EPS export as lineart or text</li>
3336 <li>Jar files are executable</li>
3337 <li>Can read in Uracil - maps to unknown residue</li>
3342 <li>Known OutOfMemory errors give warning message</li>
3343 <li>Overview window calculated more efficiently</li>
3344 <li>Several GUI bugs resolved</li>
3350 <div align="center">
3351 <strong>2.05</strong><br> 30/8/05
3356 <li>Edit and annotate in "Wrapped" view</li>
3361 <li>Several GUI bugs resolved</li>
3367 <div align="center">
3368 <strong>2.04</strong><br> 24/8/05
3373 <li>Hold down mouse wheel & scroll to change font
3379 <li>Improved JPred client reliability</li>
3380 <li>Improved loading of Jalview files</li>
3386 <div align="center">
3387 <strong>2.03</strong><br> 18/8/05
3392 <li>Set Proxy server name and port in preferences</li>
3393 <li>Multiple URL links from sequence ids</li>
3394 <li>User Defined Colours can have a scheme name and added
3396 <li>Choose to ignore gaps in consensus calculation</li>
3397 <li>Unix users can set default web browser</li>
3398 <li>Runs without GUI for batch processing</li>
3399 <li>Dynamically generated Web Service Menus</li>
3404 <li>InstallAnywhere download for Sparc Solaris</li>
3410 <div align="center">
3411 <strong>2.02</strong><br> 18/7/05
3417 <li>Copy & Paste order of sequences maintains
3418 alignment order.</li>
3424 <div align="center">
3425 <strong>2.01</strong><br> 12/7/05
3430 <li>Use delete key for deleting selection.</li>
3431 <li>Use Mouse wheel to scroll sequences.</li>
3432 <li>Help file updated to describe how to add alignment
3434 <li>Version and build date written to build properties
3436 <li>InstallAnywhere installation will check for updates
3437 at launch of Jalview.</li>
3442 <li>Delete gaps bug fixed.</li>
3443 <li>FileChooser sorts columns.</li>
3444 <li>Can remove groups one by one.</li>
3445 <li>Filechooser icons installed.</li>
3446 <li>Finder ignores return character when searching.
3447 Return key will initiate a search.<br>
3454 <div align="center">
3455 <strong>2.0</strong><br> 20/6/05
3460 <li>New codebase</li>