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;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
76 <td><div align="left">
81 <!-- JAL-1933 -->Occupancy annotation row shows number of
82 ungapped positions in each column of the alignment.
85 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
86 a calculation dialog box
89 <!-- JAL-2379 -->Revised implementation of PCA for speed
90 and memory efficiency (~30x faster)
93 <!-- JAL-2403 -->Revised implementation of sequence
94 similarity scores as used by Tree, PCA, Shading Consensus
95 and other calculations
98 <!-- JAL-2416 -->Score matrices are stored as resource
99 files within the Jalview codebase
102 <!-- JAL-2500 -->Trees computed on Sequence Feature
103 Similarity may have different topology due to increased
110 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
111 model for alignments and groups
114 <!-- JAL-384 -->Custom shading schemes created via groovy
121 <!-- JAL-2526 -->Efficiency improvements for interacting
122 with alignment and overview windows
125 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
126 via Overview or sequence motif search operations
129 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
133 <!-- JAL-2388 -->Hidden columns and sequences can be
137 <!-- JAL-2611 -->Click-drag in visible area allows fine
138 adjustment of visible position
142 <em>Data import/export</em>
145 <!-- JAL-2535 -->Posterior probability annotation from
146 Stockholm files imported as sequence associated annotation
149 <!-- JAL-2507 -->More robust per-sequence positional
150 annotation input/output via stockholm flatfile
153 <!-- JAL-2533 -->Sequence names don't include file
154 extension when importing structure files without embedded
155 names or PDB accessions
158 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
159 format sequence substitution matrices
162 <em>User Interface</em>
165 <!-- JAL-2447 --> Experimental Features Checkbox in
166 Desktop's Tools menu to hide or show untested features in
170 <!-- JAL-2547 -->Amend sequence features dialog box can be
171 opened by double clicking gaps within sequence feature
175 <!-- JAL-1476 -->Status bar message shown when not enough
176 aligned positions were available to create a 3D structure
180 <em>3D Structure</em>
183 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
184 file-based command exchange
187 <!-- JAL-2375 -->Structure chooser automatically shows
188 Cached Structures rather than querying the PDBe if
189 structures are already available for sequences
192 <!-- JAL-2520 -->Structures imported via URL are cached in
193 the Jalview project rather than downloaded again when the
197 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
198 to transfer Chimera's structure attributes as Jalview
199 features, and vice-versa (<strong>Experimental
203 <em>Web Services</em>
206 <!-- JAL-2549 -->Updated JABAWS client to v2.2
209 <!-- JAL-2335 -->Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
212 <!-- JAL-2316, -->URLs for viewing database
213 cross-references provided by identifiers.org and the
221 <!-- JAL-2344 -->FileFormatI interface for describing and
222 identifying file formats (instead of String constants)
225 <!-- JAL-2228 -->FeatureCounter script refactored for
226 efficiency when counting all displayed features (not
227 backwards compatible with 2.10.1)
230 <em>Example files</em>
233 <!-- JAL-2631 -->Graduated feature colour style example
234 included in the example feature file
237 <em>Documentation</em>
240 <!-- JAL-2339 -->Release notes reformatted for readibility
241 with the built-in Java help viewer
244 <!-- JAL-1644 -->Find documentation updated with 'search
245 sequence description' option
251 <!-- JAL-2485, -->External service integration tests for
252 Uniprot REST Free Text Search Client
255 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
258 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
263 <td><div align="left">
264 <em>Calculations</em>
267 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
268 matrix - C->R should be '-3'<br />Old matrix restored
269 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
272 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
273 and substitution matrix based Tree calculations.<br />In
274 earlier versions of Jalview, gaps matching gaps were
275 penalised, and gaps matching non-gaps penalised even more.
276 In the PCA calculation, gaps were actually treated as
277 non-gaps - so different costs were applied, which meant
278 Jalview's PCAs were different to those produced by
279 SeqSpace.<br />Jalview now treats gaps in the same way as
280 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
282 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
284 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
288 <!-- JAL-2424 -->Fixed off-by-one bug that affected
289 scaling of branch lengths for trees computed using
290 Sequence Feature Similarity.
293 <!-- JAL-2377 -->PCA calculation could hang when
294 generating output report when working with highly
298 <!-- JAL-2544 --> Sort by features includes features to
299 right of selected region when gaps present on right-hand
303 <em>User Interface</em>
306 <!-- JAL-2346 -->Reopening Colour by annotation dialog
307 doesn't reselect a specific sequence's associated
308 annotation after it was used for colouring a view
311 <!-- JAL-2419 -->Current selection lost if popup menu
312 opened on a region of alignment without groups
315 <!-- JAL-2374 -->Popup menu not always shown for regions
316 of an alignment with overlapping groups
319 <!-- JAL-2310 -->Finder double counts if both a sequence's
320 name and description match
323 <!-- JAL-2370 -->Hiding column selection containing two
324 hidden regions results in incorrect hidden regions
327 <!-- JAL-2386 -->'Apply to all groups' setting when
328 changing colour does not apply Conservation slider value
332 <!-- JAL-2373 -->Percentage identity and conservation menu
333 items do not show a tick or allow shading to be disabled
336 <!-- JAL-2385 -->Conservation shading or PID threshold
337 lost when base colourscheme changed if slider not visible
340 <!-- JAL-2547 -->Sequence features shown in tooltip for
341 gaps before start of features
344 <!-- JAL-2623 -->Graduated feature colour threshold not
345 restored to UI when feature colour is edited
348 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
349 a time when scrolling vertically in wrapped mode.
352 <!-- JAL-2630 -->Structure and alignment overview update
353 as graduate feature colour settings are modified via the
357 <!-- JAL-2034 -->Overview window doesn't always update
358 when a group defined on the alignment is resized
361 <!-- JAL-2605 -->Mouseovers on left/right scale region in
362 wrapped view result in positional status updates
366 <!-- JAL-2563 -->Status bar doesn't show position for
367 ambiguous amino acid and nucleotide symbols
370 <!-- JAL-2602 -->Copy consensus sequence failed if
371 alignment included gapped columns
374 <!-- JAL-2473 -->Minimum size set for Jalview windows so
375 widgets don't permanently disappear
378 <!-- JAL-2503 -->Cannot select or filter quantitative
379 annotation that are shown only as column labels (e.g.
380 T-Coffee column reliability scores)
383 <!-- JAL-2594 -->Exception thrown if trying to create a
384 sequence feature on gaps only
387 <!-- JAL-2504 -->Features created with 'New feature'
388 button from a Find inherit previously defined feature type
389 rather than the Find query string
392 <!-- JAL-2423 -->incorrect title in output window when
393 exporting tree calculated in Jalview
396 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
397 and then revealing them reorders sequences on the
401 <!-- JAL-964 -->Group panel in sequence feature settings
402 doesn't update to reflect available set of groups after
403 interactively adding or modifying features
406 <!-- JAL-2225 -->Sequence Database chooser unusable on
410 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
411 only excluded gaps in current sequence and ignored
418 <!-- JAL-2430 -->Hidden regions in alignment views are not
419 coloured in linked structure views
422 <!-- JAL-2421 -->Overview window visible region moves
423 erratically when hidden rows or columns are present
426 <!-- JAL-2362 -->Per-residue colourschemes applied via the
427 Structure Viewer's colour menu don't correspond to
431 <!-- JAL-2405 -->Protein specific colours only offered in
432 colour and group colour menu for protein alignments
435 <!-- JAL-2385 -->Colour threshold slider doesn't update to
436 reflect currently selected view or group's shading
440 <!-- JAL-2624 -->Feature colour thresholds not respected
441 when rendered on overview and structures when opacity at
445 <!-- JAL-2589 -->User defined gap colour not shown in
446 overview when features overlaid on alignment
449 <em>Data import/export</em>
452 <!-- JAL-2576 -->Very large alignments take a long time to
456 <!-- JAL-2507 -->Per-sequence RNA secondary structures
457 added after a sequence was imported are not written to
461 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
462 when importing RNA secondary structure via Stockholm
465 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
466 not shown in correct direction for simple pseudoknots
469 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
470 with lightGray or darkGray via features file (but can
474 <!-- JAL-2383 -->Above PID colour threshold not recovered
475 when alignment view imported from project
478 <!-- JAL-2520,JAL-2465 -->No mappings generated between
479 structure and sequences extracted from structure files
480 imported via URL and viewed in Jmol
483 <!-- JAL-2520 -->Structures loaded via URL are saved in
484 Jalview Projects rather than fetched via URL again when
485 the project is loaded and the structure viewed
488 <em>Web Services</em>
491 <!-- JAL-2519 -->EnsemblGenomes example failing after
492 release of Ensembl v.88
495 <!-- JAL-2366 -->Proxy server address and port always
496 appear enabled in Preferences->Connections
499 <!-- JAL-2461 -->DAS registry not found exceptions
500 removed from console output
503 <!-- JAL-2582 -->Cannot retrieve protein products from
504 Ensembl by Peptide ID
507 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
508 created from SIFTs, and spurious 'Couldn't open structure
509 in Chimera' errors raised after April 2017 update (problem
510 due to 'null' string rather than empty string used for
511 residues with no corresponding PDB mapping).
514 <em>Application UI</em>
517 <!-- JAL-2361 -->User Defined Colours not added to Colour
521 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
522 case' residues (button in colourscheme editor debugged and
523 new documentation and tooltips added)
526 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
527 doesn't restore group-specific text colour thresholds
530 <!-- JAL-2243 -->Feature settings panel does not update as
531 new features are added to alignment
534 <!-- JAL-2532 -->Cancel in feature settings reverts
535 changes to feature colours via the Amend features dialog
538 <!-- JAL-2506 -->Null pointer exception when attempting to
539 edit graduated feature colour via amend features dialog
543 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
544 selection menu changes colours of alignment views
547 <!-- JAL-2426 -->Spurious exceptions in console raised
548 from alignment calculation workers after alignment has
552 <!-- JAL-1608 -->Typo in selection popup menu - Create
553 groups now 'Create Group'
556 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
557 Create/Undefine group doesn't always work
560 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
561 shown again after pressing 'Cancel'
564 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
565 adjusts start position in wrap mode
568 <!-- JAL-2563 -->Status bar doesn't show positions for
569 ambiguous amino acids
572 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
573 CDS/Protein view after CDS sequences added for aligned
577 <!-- JAL-2592 -->User defined colourschemes called 'User
578 Defined' don't appear in Colours menu
584 <!-- JAL-2468 -->Switching between Nucleotide and Protein
585 score models doesn't always result in an updated PCA plot
588 <!-- JAL-2442 -->Features not rendered as transparent on
589 overview or linked structure view
592 <!-- JAL-2372 -->Colour group by conservation doesn't
596 <!-- JAL-2517 -->Hitting Cancel after applying
597 user-defined colourscheme doesn't restore original
604 <!-- JAL-2314 -->Unit test failure:
605 jalview.ws.jabaws.RNAStructExportImport setup fails
608 <!-- JAL-2307 -->Unit test failure:
609 jalview.ws.sifts.SiftsClientTest due to compatibility
610 problems with deep array comparison equality asserts in
611 successive versions of TestNG
614 <!-- JAL-2479 -->Relocated StructureChooserTest and
615 ParameterUtilsTest Unit tests to Network suite
618 <em>New Known Issues</em>
621 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
622 phase after a sequence motif find operation
625 <!-- JAL-2550 -->Importing annotation file with rows
626 containing just upper and lower case letters are
627 interpreted as WUSS rna secondary structure symbols
630 <!-- JAL-2590 -->Cannot load Newick trees from eggnog
634 <!-- JAL-2468 -->Status bar shows 'Marked x columns
635 containing features of type Highlight' when 'B' is pressed
636 to mark columns containing highlighted regions.
639 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
640 doesn't always add secondary structure annotation.
644 <td width="60" nowrap>
646 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
649 <td><div align="left">
653 <!-- JAL-98 -->Improved memory usage: sparse arrays used
654 for all consensus calculations
657 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
660 <li>Updated Jalview's Certum code signing certificate
666 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
667 set of database cross-references, sorted alphabetically
670 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
671 from database cross references. Users with custom links
672 will receive a <a href="webServices/urllinks.html#warning">warning
673 dialog</a> asking them to update their preferences.
676 <!-- JAL-2287-->Cancel button and escape listener on
677 dialog warning user about disconnecting Jalview from a
681 <!-- JAL-2320-->Jalview's Chimera control window closes if
682 the Chimera it is connected to is shut down
685 <!-- JAL-1738-->New keystroke (B) and Select highlighted
686 columns menu item to mark columns containing highlighted
687 regions (e.g. from structure selections or results of a
691 <!-- JAL-2284-->Command line option for batch-generation
692 of HTML pages rendering alignment data with the BioJS
702 <!-- JAL-2286 -->Columns with more than one modal residue
703 are not coloured or thresholded according to percent
704 identity (first observed in Jalview 2.8.2)
707 <!-- JAL-2301 -->Threonine incorrectly reported as not
711 <!-- JAL-2318 -->Updates to documentation pages (above PID
712 threshold, amino acid properties)
715 <!-- JAL-2292 -->Lower case residues in sequences are not
716 reported as mapped to residues in a structure file in the
720 <!--JAL-2324 -->Identical features with non-numeric scores
721 could be added multiple times to a sequence
724 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
725 bond features shown as two highlighted residues rather
726 than a range in linked structure views, and treated
727 correctly when selecting and computing trees from features
730 <!-- JAL-2281-->Custom URL links for database
731 cross-references are matched to database name regardless
739 <!-- JAL-2282-->Custom URL links for specific database
740 names without regular expressions also offer links from
744 <!-- JAL-2315-->Removing a single configured link in the
745 URL links pane in Connections preferences doesn't actually
746 update Jalview configuration
749 <!-- JAL-2272-->CTRL-Click on a selected region to open
750 the alignment area popup menu doesn't work on El-Capitan
753 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
754 files with similarly named sequences if dropped onto the
758 <!-- JAL-2312 -->Additional mappings are shown for PDB
759 entries where more chains exist in the PDB accession than
760 are reported in the SIFTS file
763 <!-- JAL-2317-->Certain structures do not get mapped to
764 the structure view when displayed with Chimera
767 <!-- JAL-2317-->No chains shown in the Chimera view
768 panel's View->Show Chains submenu
771 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
772 work for wrapped alignment views
775 <!--JAL-2197 -->Rename UI components for running JPred
776 predictions from 'JNet' to 'JPred'
779 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
780 corrupted when annotation panel vertical scroll is not at
784 <!--JAL-2332 -->Attempting to view structure for Hen
785 lysozyme results in a PDB Client error dialog box
788 <!-- JAL-2319 -->Structure View's mapping report switched
789 ranges for PDB and sequence for SIFTS
792 SIFTS 'Not_Observed' residues mapped to non-existant
796 <!-- <em>New Known Issues</em>
803 <td width="60" nowrap>
805 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
806 <em>25/10/2016</em></strong>
809 <td><em>Application</em>
811 <li>3D Structure chooser opens with 'Cached structures'
812 view if structures already loaded</li>
813 <li>Progress bar reports models as they are loaded to
820 <li>Colour by conservation always enabled and no tick
821 shown in menu when BLOSUM or PID shading applied</li>
822 <li>FER1_ARATH and FER2_ARATH labels were switched in
823 example sequences/projects/trees</li>
827 <li>Jalview projects with views of local PDB structure
828 files saved on Windows cannot be opened on OSX</li>
829 <li>Multiple structure views can be opened and superposed
830 without timeout for structures with multiple models or
831 multiple sequences in alignment</li>
832 <li>Cannot import or associated local PDB files without a
833 PDB ID HEADER line</li>
834 <li>RMSD is not output in Jmol console when superposition
836 <li>Drag and drop of URL from Browser fails for Linux and
837 OSX versions earlier than El Capitan</li>
838 <li>ENA client ignores invalid content from ENA server</li>
839 <li>Exceptions are not raised in console when ENA client
840 attempts to fetch non-existent IDs via Fetch DB Refs UI
842 <li>Exceptions are not raised in console when a new view
843 is created on the alignment</li>
844 <li>OSX right-click fixed for group selections: CMD-click
845 to insert/remove gaps in groups and CTRL-click to open group
848 <em>Build and deployment</em>
850 <li>URL link checker now copes with multi-line anchor
853 <em>New Known Issues</em>
855 <li>Drag and drop from URL links in browsers do not work
862 <td width="60" nowrap>
864 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
870 <!-- JAL-2124 -->Updated Spanish translations.
873 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
874 for importing structure data to Jalview. Enables mmCIF and
878 <!-- JAL-192 --->Alignment ruler shows positions relative to
882 <!-- JAL-2202 -->Position/residue shown in status bar when
883 mousing over sequence associated annotation
886 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
890 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
891 '()', canonical '[]' and invalid '{}' base pair populations
895 <!-- JAL-2092 -->Feature settings popup menu options for
896 showing or hiding columns containing a feature
899 <!-- JAL-1557 -->Edit selected group by double clicking on
900 group and sequence associated annotation labels
903 <!-- JAL-2236 -->Sequence name added to annotation label in
904 select/hide columns by annotation and colour by annotation
908 </ul> <em>Application</em>
911 <!-- JAL-2050-->Automatically hide introns when opening a
915 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
919 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
920 structure mappings with the EMBL-EBI PDBe SIFTS database
923 <!-- JAL-2079 -->Updated download sites used for Rfam and
924 Pfam sources to xfam.org
927 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
930 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
931 over sequences in Jalview
934 <!-- JAL-2027-->Support for reverse-complement coding
935 regions in ENA and EMBL
938 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
939 for record retrieval via ENA rest API
942 <!-- JAL-2027 -->Support for ENA CDS records with reverse
946 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
947 groovy script execution
950 <!-- JAL-1812 -->New 'execute Groovy script' option in an
951 alignment window's Calculate menu
954 <!-- JAL-1812 -->Allow groovy scripts that call
955 Jalview.getAlignFrames() to run in headless mode
958 <!-- JAL-2068 -->Support for creating new alignment
959 calculation workers from groovy scripts
962 <!-- JAL-1369 --->Store/restore reference sequence in
966 <!-- JAL-1803 -->Chain codes for a sequence's PDB
967 associations are now saved/restored from project
970 <!-- JAL-1993 -->Database selection dialog always shown
971 before sequence fetcher is opened
974 <!-- JAL-2183 -->Double click on an entry in Jalview's
975 database chooser opens a sequence fetcher
978 <!-- JAL-1563 -->Free-text search client for UniProt using
982 <!-- JAL-2168 -->-nonews command line parameter to prevent
983 the news reader opening
986 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
987 querying stored in preferences
990 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
994 <!-- JAL-1977-->Tooltips shown on database chooser
997 <!-- JAL-391 -->Reverse complement function in calculate
998 menu for nucleotide sequences
1001 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1002 and feature counts preserves alignment ordering (and
1003 debugged for complex feature sets).
1006 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1007 viewing structures with Jalview 2.10
1010 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1011 genome, transcript CCDS and gene ids via the Ensembl and
1012 Ensembl Genomes REST API
1015 <!-- JAL-2049 -->Protein sequence variant annotation
1016 computed for 'sequence_variant' annotation on CDS regions
1020 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1024 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1025 Ref Fetcher fails to match, or otherwise updates sequence
1026 data from external database records.
1029 <!-- JAL-2154 -->Revised Jalview Project format for
1030 efficient recovery of sequence coding and alignment
1031 annotation relationships.
1033 </ul> <!-- <em>Applet</em>
1044 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1048 <!-- JAL-2018-->Export features in Jalview format (again)
1049 includes graduated colourschemes
1052 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1053 working with big alignments and lots of hidden columns
1056 <!-- JAL-2053-->Hidden column markers not always rendered
1057 at right of alignment window
1060 <!-- JAL-2067 -->Tidied up links in help file table of
1064 <!-- JAL-2072 -->Feature based tree calculation not shown
1068 <!-- JAL-2075 -->Hidden columns ignored during feature
1069 based tree calculation
1072 <!-- JAL-2065 -->Alignment view stops updating when show
1073 unconserved enabled for group on alignment
1076 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1080 <!-- JAL-2146 -->Alignment column in status incorrectly
1081 shown as "Sequence position" when mousing over
1085 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1086 hidden columns present
1089 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1090 user created annotation added to alignment
1093 <!-- JAL-1841 -->RNA Structure consensus only computed for
1094 '()' base pair annotation
1097 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1098 in zero scores for all base pairs in RNA Structure
1102 <!-- JAL-2174-->Extend selection with columns containing
1106 <!-- JAL-2275 -->Pfam format writer puts extra space at
1107 beginning of sequence
1110 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1114 <!-- JAL-2238 -->Cannot create groups on an alignment from
1115 from a tree when t-coffee scores are shown
1118 <!-- JAL-1836,1967 -->Cannot import and view PDB
1119 structures with chains containing negative resnums (4q4h)
1122 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1126 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1127 to Clustal, PIR and PileUp output
1130 <!-- JAL-2008 -->Reordering sequence features that are
1131 not visible causes alignment window to repaint
1134 <!-- JAL-2006 -->Threshold sliders don't work in
1135 graduated colour and colour by annotation row for e-value
1136 scores associated with features and annotation rows
1139 <!-- JAL-1797 -->amino acid physicochemical conservation
1140 calculation should be case independent
1143 <!-- JAL-2173 -->Remove annotation also updates hidden
1147 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1148 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1149 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1152 <!-- JAL-2065 -->Null pointer exceptions and redraw
1153 problems when reference sequence defined and 'show
1154 non-conserved' enabled
1157 <!-- JAL-1306 -->Quality and Conservation are now shown on
1158 load even when Consensus calculation is disabled
1161 <!-- JAL-1932 -->Remove right on penultimate column of
1162 alignment does nothing
1165 <em>Application</em>
1168 <!-- JAL-1552-->URLs and links can't be imported by
1169 drag'n'drop on OSX when launched via webstart (note - not
1170 yet fixed for El Capitan)
1173 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1174 output when running on non-gb/us i18n platforms
1177 <!-- JAL-1944 -->Error thrown when exporting a view with
1178 hidden sequences as flat-file alignment
1181 <!-- JAL-2030-->InstallAnywhere distribution fails when
1185 <!-- JAL-2080-->Jalview very slow to launch via webstart
1186 (also hotfix for 2.9.0b2)
1189 <!-- JAL-2085 -->Cannot save project when view has a
1190 reference sequence defined
1193 <!-- JAL-1011 -->Columns are suddenly selected in other
1194 alignments and views when revealing hidden columns
1197 <!-- JAL-1989 -->Hide columns not mirrored in complement
1198 view in a cDNA/Protein splitframe
1201 <!-- JAL-1369 -->Cannot save/restore representative
1202 sequence from project when only one sequence is
1206 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1207 in Structure Chooser
1210 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1211 structure consensus didn't refresh annotation panel
1214 <!-- JAL-1962 -->View mapping in structure view shows
1215 mappings between sequence and all chains in a PDB file
1218 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1219 dialogs format columns correctly, don't display array
1220 data, sort columns according to type
1223 <!-- JAL-1975 -->Export complete shown after destination
1224 file chooser is cancelled during an image export
1227 <!-- JAL-2025 -->Error when querying PDB Service with
1228 sequence name containing special characters
1231 <!-- JAL-2024 -->Manual PDB structure querying should be
1235 <!-- JAL-2104 -->Large tooltips with broken HTML
1236 formatting don't wrap
1239 <!-- JAL-1128 -->Figures exported from wrapped view are
1240 truncated so L looks like I in consensus annotation
1243 <!-- JAL-2003 -->Export features should only export the
1244 currently displayed features for the current selection or
1248 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1249 after fetching cross-references, and restoring from
1253 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1254 followed in the structure viewer
1257 <!-- JAL-2163 -->Titles for individual alignments in
1258 splitframe not restored from project
1261 <!-- JAL-2145 -->missing autocalculated annotation at
1262 trailing end of protein alignment in transcript/product
1263 splitview when pad-gaps not enabled by default
1266 <!-- JAL-1797 -->amino acid physicochemical conservation
1270 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1271 article has been read (reopened issue due to
1272 internationalisation problems)
1275 <!-- JAL-1960 -->Only offer PDB structures in structure
1276 viewer based on sequence name, PDB and UniProt
1281 <!-- JAL-1976 -->No progress bar shown during export of
1285 <!-- JAL-2213 -->Structures not always superimposed after
1286 multiple structures are shown for one or more sequences.
1289 <!-- JAL-1370 -->Reference sequence characters should not
1290 be replaced with '.' when 'Show unconserved' format option
1294 <!-- JAL-1823 -->Cannot specify chain code when entering
1295 specific PDB id for sequence
1298 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1299 'Export hidden sequences' is enabled, but 'export hidden
1300 columns' is disabled.
1303 <!--JAL-2026-->Best Quality option in structure chooser
1304 selects lowest rather than highest resolution structures
1308 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1309 to sequence mapping in 'View Mappings' report
1312 <!-- JAL-2284 -->Unable to read old Jalview projects that
1313 contain non-XML data added after Jalvew wrote project.
1316 <!-- JAL-2118 -->Newly created annotation row reorders
1317 after clicking on it to create new annotation for a
1320 <!-- may exclude, this is an external service stability issue JAL-1941
1321 -- > RNA 3D structure not added via DSSR service</li> -->
1326 <!-- JAL-2151 -->Incorrect columns are selected when
1327 hidden columns present before start of sequence
1330 <!-- JAL-1986 -->Missing dependencies on applet pages
1334 <!-- JAL-1947 -->Overview pixel size changes when
1335 sequences are hidden in applet
1338 <!-- JAL-1996 -->Updated instructions for applet
1339 deployment on examples pages.
1346 <td width="60" nowrap>
1347 <div align="center">
1348 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1349 <em>16/10/2015</em></strong>
1352 <td><em>General</em>
1354 <li>Time stamps for signed Jalview application and applet
1359 <em>Application</em>
1361 <li>Duplicate group consensus and conservation rows
1362 shown when tree is partitioned</li>
1363 <li>Erratic behaviour when tree partitions made with
1364 multiple cDNA/Protein split views</li>
1370 <td width="60" nowrap>
1371 <div align="center">
1372 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1373 <em>8/10/2015</em></strong>
1376 <td><em>General</em>
1378 <li>Updated Spanish translations of localized text for
1380 </ul> <em>Application</em>
1382 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1383 <li>Signed OSX InstallAnywhere installer<br></li>
1384 <li>Support for per-sequence based annotations in BioJSON</li>
1385 </ul> <em>Applet</em>
1387 <li>Split frame example added to applet examples page</li>
1388 </ul> <em>Build and Deployment</em>
1391 <!-- JAL-1888 -->New ant target for running Jalview's test
1399 <li>Mapping of cDNA to protein in split frames
1400 incorrect when sequence start > 1</li>
1401 <li>Broken images in filter column by annotation dialog
1403 <li>Feature colours not parsed from features file</li>
1404 <li>Exceptions and incomplete link URLs recovered when
1405 loading a features file containing HTML tags in feature
1409 <em>Application</em>
1411 <li>Annotations corrupted after BioJS export and
1413 <li>Incorrect sequence limits after Fetch DB References
1414 with 'trim retrieved sequences'</li>
1415 <li>Incorrect warning about deleting all data when
1416 deleting selected columns</li>
1417 <li>Patch to build system for shipping properly signed
1418 JNLP templates for webstart launch</li>
1419 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1420 unreleased structures for download or viewing</li>
1421 <li>Tab/space/return keystroke operation of EMBL-PDBe
1422 fetcher/viewer dialogs works correctly</li>
1423 <li>Disabled 'minimise' button on Jalview windows
1424 running on OSX to workaround redraw hang bug</li>
1425 <li>Split cDNA/Protein view position and geometry not
1426 recovered from jalview project</li>
1427 <li>Initial enabled/disabled state of annotation menu
1428 sorter 'show autocalculated first/last' corresponds to
1430 <li>Restoring of Clustal, RNA Helices and T-Coffee
1431 color schemes from BioJSON</li>
1435 <li>Reorder sequences mirrored in cDNA/Protein split
1437 <li>Applet with Jmol examples not loading correctly</li>
1443 <td><div align="center">
1444 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1446 <td><em>General</em>
1448 <li>Linked visualisation and analysis of DNA and Protein
1451 <li>Translated cDNA alignments shown as split protein
1452 and DNA alignment views</li>
1453 <li>Codon consensus annotation for linked protein and
1454 cDNA alignment views</li>
1455 <li>Link cDNA or Protein product sequences by loading
1456 them onto Protein or cDNA alignments</li>
1457 <li>Reconstruct linked cDNA alignment from aligned
1458 protein sequences</li>
1461 <li>Jmol integration updated to Jmol v14.2.14</li>
1462 <li>Import and export of Jalview alignment views as <a
1463 href="features/bioJsonFormat.html">BioJSON</a></li>
1464 <li>New alignment annotation file statements for
1465 reference sequences and marking hidden columns</li>
1466 <li>Reference sequence based alignment shading to
1467 highlight variation</li>
1468 <li>Select or hide columns according to alignment
1470 <li>Find option for locating sequences by description</li>
1471 <li>Conserved physicochemical properties shown in amino
1472 acid conservation row</li>
1473 <li>Alignments can be sorted by number of RNA helices</li>
1474 </ul> <em>Application</em>
1476 <li>New cDNA/Protein analysis capabilities
1478 <li>Get Cross-References should open a Split Frame
1479 view with cDNA/Protein</li>
1480 <li>Detect when nucleotide sequences and protein
1481 sequences are placed in the same alignment</li>
1482 <li>Split cDNA/Protein views are saved in Jalview
1487 <li>Use REST API to talk to Chimera</li>
1488 <li>Selected regions in Chimera are highlighted in linked
1489 Jalview windows</li>
1491 <li>VARNA RNA viewer updated to v3.93</li>
1492 <li>VARNA views are saved in Jalview Projects</li>
1493 <li>Pseudoknots displayed as Jalview RNA annotation can
1494 be shown in VARNA</li>
1496 <li>Make groups for selection uses marked columns as well
1497 as the active selected region</li>
1499 <li>Calculate UPGMA and NJ trees using sequence feature
1501 <li>New Export options
1503 <li>New Export Settings dialog to control hidden
1504 region export in flat file generation</li>
1506 <li>Export alignment views for display with the <a
1507 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1509 <li>Export scrollable SVG in HTML page</li>
1510 <li>Optional embedding of BioJSON data when exporting
1511 alignment figures to HTML</li>
1513 <li>3D structure retrieval and display
1515 <li>Free text and structured queries with the PDBe
1517 <li>PDBe Search API based discovery and selection of
1518 PDB structures for a sequence set</li>
1522 <li>JPred4 employed for protein secondary structure
1524 <li>Hide Insertions menu option to hide unaligned columns
1525 for one or a group of sequences</li>
1526 <li>Automatically hide insertions in alignments imported
1527 from the JPred4 web server</li>
1528 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1529 system on OSX<br />LGPL libraries courtesy of <a
1530 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1532 <li>changed 'View nucleotide structure' submenu to 'View
1533 VARNA 2D Structure'</li>
1534 <li>change "View protein structure" menu option to "3D
1537 </ul> <em>Applet</em>
1539 <li>New layout for applet example pages</li>
1540 <li>New parameters to enable SplitFrame view
1541 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1542 <li>New example demonstrating linked viewing of cDNA and
1543 Protein alignments</li>
1544 </ul> <em>Development and deployment</em>
1546 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1547 <li>Include installation type and git revision in build
1548 properties and console log output</li>
1549 <li>Jalview Github organisation, and new github site for
1550 storing BioJsMSA Templates</li>
1551 <li>Jalview's unit tests now managed with TestNG</li>
1554 <!-- <em>General</em>
1556 </ul> --> <!-- issues resolved --> <em>Application</em>
1558 <li>Escape should close any open find dialogs</li>
1559 <li>Typo in select-by-features status report</li>
1560 <li>Consensus RNA secondary secondary structure
1561 predictions are not highlighted in amber</li>
1562 <li>Missing gap character in v2.7 example file means
1563 alignment appears unaligned when pad-gaps is not enabled</li>
1564 <li>First switch to RNA Helices colouring doesn't colour
1565 associated structure views</li>
1566 <li>ID width preference option is greyed out when auto
1567 width checkbox not enabled</li>
1568 <li>Stopped a warning dialog from being shown when
1569 creating user defined colours</li>
1570 <li>'View Mapping' in structure viewer shows sequence
1571 mappings for just that viewer's sequences</li>
1572 <li>Workaround for superposing PDB files containing
1573 multiple models in Chimera</li>
1574 <li>Report sequence position in status bar when hovering
1575 over Jmol structure</li>
1576 <li>Cannot output gaps as '.' symbols with Selection ->
1577 output to text box</li>
1578 <li>Flat file exports of alignments with hidden columns
1579 have incorrect sequence start/end</li>
1580 <li>'Aligning' a second chain to a Chimera structure from
1582 <li>Colour schemes applied to structure viewers don't
1583 work for nucleotide</li>
1584 <li>Loading/cut'n'pasting an empty or invalid file leads
1585 to a grey/invisible alignment window</li>
1586 <li>Exported Jpred annotation from a sequence region
1587 imports to different position</li>
1588 <li>Space at beginning of sequence feature tooltips shown
1589 on some platforms</li>
1590 <li>Chimera viewer 'View | Show Chain' menu is not
1592 <li>'New View' fails with a Null Pointer Exception in
1593 console if Chimera has been opened</li>
1594 <li>Mouseover to Chimera not working</li>
1595 <li>Miscellaneous ENA XML feature qualifiers not
1597 <li>NPE in annotation renderer after 'Extract Scores'</li>
1598 <li>If two structures in one Chimera window, mouseover of
1599 either sequence shows on first structure</li>
1600 <li>'Show annotations' options should not make
1601 non-positional annotations visible</li>
1602 <li>Subsequence secondary structure annotation not shown
1603 in right place after 'view flanking regions'</li>
1604 <li>File Save As type unset when current file format is
1606 <li>Save as '.jar' option removed for saving Jalview
1608 <li>Colour by Sequence colouring in Chimera more
1610 <li>Cannot 'add reference annotation' for a sequence in
1611 several views on same alignment</li>
1612 <li>Cannot show linked products for EMBL / ENA records</li>
1613 <li>Jalview's tooltip wraps long texts containing no
1615 </ul> <em>Applet</em>
1617 <li>Jmol to JalviewLite mouseover/link not working</li>
1618 <li>JalviewLite can't import sequences with ID
1619 descriptions containing angle brackets</li>
1620 </ul> <em>General</em>
1622 <li>Cannot export and reimport RNA secondary structure
1623 via jalview annotation file</li>
1624 <li>Random helix colour palette for colour by annotation
1625 with RNA secondary structure</li>
1626 <li>Mouseover to cDNA from STOP residue in protein
1627 translation doesn't work.</li>
1628 <li>hints when using the select by annotation dialog box</li>
1629 <li>Jmol alignment incorrect if PDB file has alternate CA
1631 <li>FontChooser message dialog appears to hang after
1632 choosing 1pt font</li>
1633 <li>Peptide secondary structure incorrectly imported from
1634 annotation file when annotation display text includes 'e' or
1636 <li>Cannot set colour of new feature type whilst creating
1638 <li>cDNA translation alignment should not be sequence
1639 order dependent</li>
1640 <li>'Show unconserved' doesn't work for lower case
1642 <li>Nucleotide ambiguity codes involving R not recognised</li>
1643 </ul> <em>Deployment and Documentation</em>
1645 <li>Applet example pages appear different to the rest of
1646 www.jalview.org</li>
1647 </ul> <em>Application Known issues</em>
1649 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1650 <li>Misleading message appears after trying to delete
1652 <li>Jalview icon not shown in dock after InstallAnywhere
1653 version launches</li>
1654 <li>Fetching EMBL reference for an RNA sequence results
1655 fails with a sequence mismatch</li>
1656 <li>Corrupted or unreadable alignment display when
1657 scrolling alignment to right</li>
1658 <li>ArrayIndexOutOfBoundsException thrown when remove
1659 empty columns called on alignment with ragged gapped ends</li>
1660 <li>auto calculated alignment annotation rows do not get
1661 placed above or below non-autocalculated rows</li>
1662 <li>Jalview dekstop becomes sluggish at full screen in
1663 ultra-high resolution</li>
1664 <li>Cannot disable consensus calculation independently of
1665 quality and conservation</li>
1666 <li>Mouseover highlighting between cDNA and protein can
1667 become sluggish with more than one splitframe shown</li>
1668 </ul> <em>Applet Known Issues</em>
1670 <li>Core PDB parsing code requires Jmol</li>
1671 <li>Sequence canvas panel goes white when alignment
1672 window is being resized</li>
1678 <td><div align="center">
1679 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1681 <td><em>General</em>
1683 <li>Updated Java code signing certificate donated by
1685 <li>Features and annotation preserved when performing
1686 pairwise alignment</li>
1687 <li>RNA pseudoknot annotation can be
1688 imported/exported/displayed</li>
1689 <li>'colour by annotation' can colour by RNA and
1690 protein secondary structure</li>
1691 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1692 post-hoc with 2.9 release</em>)
1695 </ul> <em>Application</em>
1697 <li>Extract and display secondary structure for sequences
1698 with 3D structures</li>
1699 <li>Support for parsing RNAML</li>
1700 <li>Annotations menu for layout
1702 <li>sort sequence annotation rows by alignment</li>
1703 <li>place sequence annotation above/below alignment
1706 <li>Output in Stockholm format</li>
1707 <li>Internationalisation: improved Spanish (es)
1709 <li>Structure viewer preferences tab</li>
1710 <li>Disorder and Secondary Structure annotation tracks
1711 shared between alignments</li>
1712 <li>UCSF Chimera launch and linked highlighting from
1714 <li>Show/hide all sequence associated annotation rows for
1715 all or current selection</li>
1716 <li>disorder and secondary structure predictions
1717 available as dataset annotation</li>
1718 <li>Per-sequence rna helices colouring</li>
1721 <li>Sequence database accessions imported when fetching
1722 alignments from Rfam</li>
1723 <li>update VARNA version to 3.91</li>
1725 <li>New groovy scripts for exporting aligned positions,
1726 conservation values, and calculating sum of pairs scores.</li>
1727 <li>Command line argument to set default JABAWS server</li>
1728 <li>include installation type in build properties and
1729 console log output</li>
1730 <li>Updated Jalview project format to preserve dataset
1734 <!-- issues resolved --> <em>Application</em>
1736 <li>Distinguish alignment and sequence associated RNA
1737 structure in structure->view->VARNA</li>
1738 <li>Raise dialog box if user deletes all sequences in an
1740 <li>Pressing F1 results in documentation opening twice</li>
1741 <li>Sequence feature tooltip is wrapped</li>
1742 <li>Double click on sequence associated annotation
1743 selects only first column</li>
1744 <li>Redundancy removal doesn't result in unlinked
1745 leaves shown in tree</li>
1746 <li>Undos after several redundancy removals don't undo
1748 <li>Hide sequence doesn't hide associated annotation</li>
1749 <li>User defined colours dialog box too big to fit on
1750 screen and buttons not visible</li>
1751 <li>author list isn't updated if already written to
1752 Jalview properties</li>
1753 <li>Popup menu won't open after retrieving sequence
1755 <li>File open window for associate PDB doesn't open</li>
1756 <li>Left-then-right click on a sequence id opens a
1757 browser search window</li>
1758 <li>Cannot open sequence feature shading/sort popup menu
1759 in feature settings dialog</li>
1760 <li>better tooltip placement for some areas of Jalview
1762 <li>Allow addition of JABAWS Server which doesn't
1763 pass validation</li>
1764 <li>Web services parameters dialog box is too large to
1766 <li>Muscle nucleotide alignment preset obscured by
1768 <li>JABAWS preset submenus don't contain newly
1769 defined user preset</li>
1770 <li>MSA web services warns user if they were launched
1771 with invalid input</li>
1772 <li>Jalview cannot contact DAS Registy when running on
1775 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1776 'Superpose with' submenu not shown when new view
1780 </ul> <!-- <em>Applet</em>
1782 </ul> <em>General</em>
1784 </ul>--> <em>Deployment and Documentation</em>
1786 <li>2G and 1G options in launchApp have no effect on
1787 memory allocation</li>
1788 <li>launchApp service doesn't automatically open
1789 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1791 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1792 InstallAnywhere reports cannot find valid JVM when Java
1793 1.7_055 is available
1795 </ul> <em>Application Known issues</em>
1798 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1799 corrupted or unreadable alignment display when scrolling
1803 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1804 retrieval fails but progress bar continues for DAS retrieval
1805 with large number of ID
1808 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1809 flatfile output of visible region has incorrect sequence
1813 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1814 rna structure consensus doesn't update when secondary
1815 structure tracks are rearranged
1818 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1819 invalid rna structure positional highlighting does not
1820 highlight position of invalid base pairs
1823 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1824 out of memory errors are not raised when saving Jalview
1825 project from alignment window file menu
1828 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1829 Switching to RNA Helices colouring doesn't propagate to
1833 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1834 colour by RNA Helices not enabled when user created
1835 annotation added to alignment
1838 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1839 Jalview icon not shown on dock in Mountain Lion/Webstart
1841 </ul> <em>Applet Known Issues</em>
1844 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1845 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1848 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1849 Jalview and Jmol example not compatible with IE9
1852 <li>Sort by annotation score doesn't reverse order
1858 <td><div align="center">
1859 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1862 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1865 <li>Internationalisation of user interface (usually
1866 called i18n support) and translation for Spanish locale</li>
1867 <li>Define/Undefine group on current selection with
1868 Ctrl-G/Shift Ctrl-G</li>
1869 <li>Improved group creation/removal options in
1870 alignment/sequence Popup menu</li>
1871 <li>Sensible precision for symbol distribution
1872 percentages shown in logo tooltip.</li>
1873 <li>Annotation panel height set according to amount of
1874 annotation when alignment first opened</li>
1875 </ul> <em>Application</em>
1877 <li>Interactive consensus RNA secondary structure
1878 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1879 <li>Select columns containing particular features from
1880 Feature Settings dialog</li>
1881 <li>View all 'representative' PDB structures for selected
1883 <li>Update Jalview project format:
1885 <li>New file extension for Jalview projects '.jvp'</li>
1886 <li>Preserve sequence and annotation dataset (to
1887 store secondary structure annotation,etc)</li>
1888 <li>Per group and alignment annotation and RNA helix
1892 <li>New similarity measures for PCA and Tree calculation
1894 <li>Experimental support for retrieval and viewing of
1895 flanking regions for an alignment</li>
1899 <!-- issues resolved --> <em>Application</em>
1901 <li>logo keeps spinning and status remains at queued or
1902 running after job is cancelled</li>
1903 <li>cannot export features from alignments imported from
1904 Jalview/VAMSAS projects</li>
1905 <li>Buggy slider for web service parameters that take
1907 <li>Newly created RNA secondary structure line doesn't
1908 have 'display all symbols' flag set</li>
1909 <li>T-COFFEE alignment score shading scheme and other
1910 annotation shading not saved in Jalview project</li>
1911 <li>Local file cannot be loaded in freshly downloaded
1913 <li>Jalview icon not shown on dock in Mountain
1915 <li>Load file from desktop file browser fails</li>
1916 <li>Occasional NPE thrown when calculating large trees</li>
1917 <li>Cannot reorder or slide sequences after dragging an
1918 alignment onto desktop</li>
1919 <li>Colour by annotation dialog throws NPE after using
1920 'extract scores' function</li>
1921 <li>Loading/cut'n'pasting an empty file leads to a grey
1922 alignment window</li>
1923 <li>Disorder thresholds rendered incorrectly after
1924 performing IUPred disorder prediction</li>
1925 <li>Multiple group annotated consensus rows shown when
1926 changing 'normalise logo' display setting</li>
1927 <li>Find shows blank dialog after 'finished searching' if
1928 nothing matches query</li>
1929 <li>Null Pointer Exceptions raised when sorting by
1930 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1932 <li>Errors in Jmol console when structures in alignment
1933 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1935 <li>Not all working JABAWS services are shown in
1937 <li>JAVAWS version of Jalview fails to launch with
1938 'invalid literal/length code'</li>
1939 <li>Annotation/RNA Helix colourschemes cannot be applied
1940 to alignment with groups (actually fixed in 2.8.0b1)</li>
1941 <li>RNA Helices and T-Coffee Scores available as default
1944 </ul> <em>Applet</em>
1946 <li>Remove group option is shown even when selection is
1948 <li>Apply to all groups ticked but colourscheme changes
1949 don't affect groups</li>
1950 <li>Documented RNA Helices and T-Coffee Scores as valid
1951 colourscheme name</li>
1952 <li>Annotation labels drawn on sequence IDs when
1953 Annotation panel is not displayed</li>
1954 <li>Increased font size for dropdown menus on OSX and
1955 embedded windows</li>
1956 </ul> <em>Other</em>
1958 <li>Consensus sequence for alignments/groups with a
1959 single sequence were not calculated</li>
1960 <li>annotation files that contain only groups imported as
1961 annotation and junk sequences</li>
1962 <li>Fasta files with sequences containing '*' incorrectly
1963 recognised as PFAM or BLC</li>
1964 <li>conservation/PID slider apply all groups option
1965 doesn't affect background (2.8.0b1)
1967 <li>redundancy highlighting is erratic at 0% and 100%</li>
1968 <li>Remove gapped columns fails for sequences with ragged
1970 <li>AMSA annotation row with leading spaces is not
1971 registered correctly on import</li>
1972 <li>Jalview crashes when selecting PCA analysis for
1973 certain alignments</li>
1974 <li>Opening the colour by annotation dialog for an
1975 existing annotation based 'use original colours'
1976 colourscheme loses original colours setting</li>
1981 <td><div align="center">
1982 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1983 <em>30/1/2014</em></strong>
1987 <li>Trusted certificates for JalviewLite applet and
1988 Jalview Desktop application<br />Certificate was donated by
1989 <a href="https://www.certum.eu">Certum</a> to the Jalview
1990 open source project).
1992 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
1993 <li>Output in Stockholm format</li>
1994 <li>Allow import of data from gzipped files</li>
1995 <li>Export/import group and sequence associated line
1996 graph thresholds</li>
1997 <li>Nucleotide substitution matrix that supports RNA and
1998 ambiguity codes</li>
1999 <li>Allow disorder predictions to be made on the current
2000 selection (or visible selection) in the same way that JPred
2002 <li>Groovy scripting for headless Jalview operation</li>
2003 </ul> <em>Other improvements</em>
2005 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2006 <li>COMBINE statement uses current SEQUENCE_REF and
2007 GROUP_REF scope to group annotation rows</li>
2008 <li>Support '' style escaping of quotes in Newick
2010 <li>Group options for JABAWS service by command line name</li>
2011 <li>Empty tooltip shown for JABA service options with a
2012 link but no description</li>
2013 <li>Select primary source when selecting authority in
2014 database fetcher GUI</li>
2015 <li>Add .mfa to FASTA file extensions recognised by
2017 <li>Annotation label tooltip text wrap</li>
2022 <li>Slow scrolling when lots of annotation rows are
2024 <li>Lots of NPE (and slowness) after creating RNA
2025 secondary structure annotation line</li>
2026 <li>Sequence database accessions not imported when
2027 fetching alignments from Rfam</li>
2028 <li>Incorrect SHMR submission for sequences with
2030 <li>View all structures does not always superpose
2032 <li>Option widgets in service parameters not updated to
2033 reflect user or preset settings</li>
2034 <li>Null pointer exceptions for some services without
2035 presets or adjustable parameters</li>
2036 <li>Discover PDB IDs entry in structure menu doesn't
2037 discover PDB xRefs</li>
2038 <li>Exception encountered while trying to retrieve
2039 features with DAS</li>
2040 <li>Lowest value in annotation row isn't coloured
2041 when colour by annotation (per sequence) is coloured</li>
2042 <li>Keyboard mode P jumps to start of gapped region when
2043 residue follows a gap</li>
2044 <li>Jalview appears to hang importing an alignment with
2045 Wrap as default or after enabling Wrap</li>
2046 <li>'Right click to add annotations' message
2047 shown in wrap mode when no annotations present</li>
2048 <li>Disorder predictions fail with NPE if no automatic
2049 annotation already exists on alignment</li>
2050 <li>oninit javascript function should be called after
2051 initialisation completes</li>
2052 <li>Remove redundancy after disorder prediction corrupts
2053 alignment window display</li>
2054 <li>Example annotation file in documentation is invalid</li>
2055 <li>Grouped line graph annotation rows are not exported
2056 to annotation file</li>
2057 <li>Multi-harmony analysis cannot be run when only two
2059 <li>Cannot create multiple groups of line graphs with
2060 several 'combine' statements in annotation file</li>
2061 <li>Pressing return several times causes Number Format
2062 exceptions in keyboard mode</li>
2063 <li>Multi-harmony (SHMMR) method doesn't submit
2064 correct partitions for input data</li>
2065 <li>Translation from DNA to Amino Acids fails</li>
2066 <li>Jalview fail to load newick tree with quoted label</li>
2067 <li>--headless flag isn't understood</li>
2068 <li>ClassCastException when generating EPS in headless
2070 <li>Adjusting sequence-associated shading threshold only
2071 changes one row's threshold</li>
2072 <li>Preferences and Feature settings panel panel
2073 doesn't open</li>
2074 <li>hide consensus histogram also hides conservation and
2075 quality histograms</li>
2080 <td><div align="center">
2081 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2083 <td><em>Application</em>
2085 <li>Support for JABAWS 2.0 Services (AACon alignment
2086 conservation, protein disorder and Clustal Omega)</li>
2087 <li>JABAWS server status indicator in Web Services
2089 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2090 in Jalview alignment window</li>
2091 <li>Updated Jalview build and deploy framework for OSX
2092 mountain lion, windows 7, and 8</li>
2093 <li>Nucleotide substitution matrix for PCA that supports
2094 RNA and ambiguity codes</li>
2096 <li>Improved sequence database retrieval GUI</li>
2097 <li>Support fetching and database reference look up
2098 against multiple DAS sources (Fetch all from in 'fetch db
2100 <li>Jalview project improvements
2102 <li>Store and retrieve the 'belowAlignment'
2103 flag for annotation</li>
2104 <li>calcId attribute to group annotation rows on the
2106 <li>Store AACon calculation settings for a view in
2107 Jalview project</li>
2111 <li>horizontal scrolling gesture support</li>
2112 <li>Visual progress indicator when PCA calculation is
2114 <li>Simpler JABA web services menus</li>
2115 <li>visual indication that web service results are still
2116 being retrieved from server</li>
2117 <li>Serialise the dialogs that are shown when Jalview
2118 starts up for first time</li>
2119 <li>Jalview user agent string for interacting with HTTP
2121 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2123 <li>Examples directory and Groovy library included in
2124 InstallAnywhere distribution</li>
2125 </ul> <em>Applet</em>
2127 <li>RNA alignment and secondary structure annotation
2128 visualization applet example</li>
2129 </ul> <em>General</em>
2131 <li>Normalise option for consensus sequence logo</li>
2132 <li>Reset button in PCA window to return dimensions to
2134 <li>Allow seqspace or Jalview variant of alignment PCA
2136 <li>PCA with either nucleic acid and protein substitution
2138 <li>Allow windows containing HTML reports to be exported
2140 <li>Interactive display and editing of RNA secondary
2141 structure contacts</li>
2142 <li>RNA Helix Alignment Colouring</li>
2143 <li>RNA base pair logo consensus</li>
2144 <li>Parse sequence associated secondary structure
2145 information in Stockholm files</li>
2146 <li>HTML Export database accessions and annotation
2147 information presented in tooltip for sequences</li>
2148 <li>Import secondary structure from LOCARNA clustalw
2149 style RNA alignment files</li>
2150 <li>import and visualise T-COFFEE quality scores for an
2152 <li>'colour by annotation' per sequence option to
2153 shade each sequence according to its associated alignment
2155 <li>New Jalview Logo</li>
2156 </ul> <em>Documentation and Development</em>
2158 <li>documentation for score matrices used in Jalview</li>
2159 <li>New Website!</li>
2161 <td><em>Application</em>
2163 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2164 wsdbfetch REST service</li>
2165 <li>Stop windows being moved outside desktop on OSX</li>
2166 <li>Filetype associations not installed for webstart
2168 <li>Jalview does not always retrieve progress of a JABAWS
2169 job execution in full once it is complete</li>
2170 <li>revise SHMR RSBS definition to ensure alignment is
2171 uploaded via ali_file parameter</li>
2172 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2173 <li>View all structures superposed fails with exception</li>
2174 <li>Jnet job queues forever if a very short sequence is
2175 submitted for prediction</li>
2176 <li>Cut and paste menu not opened when mouse clicked on
2178 <li>Putting fractional value into integer text box in
2179 alignment parameter dialog causes Jalview to hang</li>
2180 <li>Structure view highlighting doesn't work on
2182 <li>View all structures fails with exception shown in
2184 <li>Characters in filename associated with PDBEntry not
2185 escaped in a platform independent way</li>
2186 <li>Jalview desktop fails to launch with exception when
2188 <li>Tree calculation reports 'you must have 2 or more
2189 sequences selected' when selection is empty</li>
2190 <li>Jalview desktop fails to launch with jar signature
2191 failure when java web start temporary file caching is
2193 <li>DAS Sequence retrieval with range qualification
2194 results in sequence xref which includes range qualification</li>
2195 <li>Errors during processing of command line arguments
2196 cause progress bar (JAL-898) to be removed</li>
2197 <li>Replace comma for semi-colon option not disabled for
2198 DAS sources in sequence fetcher</li>
2199 <li>Cannot close news reader when JABAWS server warning
2200 dialog is shown</li>
2201 <li>Option widgets not updated to reflect user settings</li>
2202 <li>Edited sequence not submitted to web service</li>
2203 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2204 <li>InstallAnywhere installer doesn't unpack and run
2205 on OSX Mountain Lion</li>
2206 <li>Annotation panel not given a scroll bar when
2207 sequences with alignment annotation are pasted into the
2209 <li>Sequence associated annotation rows not associated
2210 when loaded from Jalview project</li>
2211 <li>Browser launch fails with NPE on java 1.7</li>
2212 <li>JABAWS alignment marked as finished when job was
2213 cancelled or job failed due to invalid input</li>
2214 <li>NPE with v2.7 example when clicking on Tree
2215 associated with all views</li>
2216 <li>Exceptions when copy/paste sequences with grouped
2217 annotation rows to new window</li>
2218 </ul> <em>Applet</em>
2220 <li>Sequence features are momentarily displayed before
2221 they are hidden using hidefeaturegroups applet parameter</li>
2222 <li>loading features via javascript API automatically
2223 enables feature display</li>
2224 <li>scrollToColumnIn javascript API method doesn't
2226 </ul> <em>General</em>
2228 <li>Redundancy removal fails for rna alignment</li>
2229 <li>PCA calculation fails when sequence has been selected
2230 and then deselected</li>
2231 <li>PCA window shows grey box when first opened on OSX</li>
2232 <li>Letters coloured pink in sequence logo when alignment
2233 coloured with clustalx</li>
2234 <li>Choosing fonts without letter symbols defined causes
2235 exceptions and redraw errors</li>
2236 <li>Initial PCA plot view is not same as manually
2237 reconfigured view</li>
2238 <li>Grouped annotation graph label has incorrect line
2240 <li>Grouped annotation graph label display is corrupted
2241 for lots of labels</li>
2246 <div align="center">
2247 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2250 <td><em>Application</em>
2252 <li>Jalview Desktop News Reader</li>
2253 <li>Tweaked default layout of web services menu</li>
2254 <li>View/alignment association menu to enable user to
2255 easily specify which alignment a multi-structure view takes
2256 its colours/correspondences from</li>
2257 <li>Allow properties file location to be specified as URL</li>
2258 <li>Extend Jalview project to preserve associations
2259 between many alignment views and a single Jmol display</li>
2260 <li>Store annotation row height in Jalview project file</li>
2261 <li>Annotation row column label formatting attributes
2262 stored in project file</li>
2263 <li>Annotation row order for auto-calculated annotation
2264 rows preserved in Jalview project file</li>
2265 <li>Visual progress indication when Jalview state is
2266 saved using Desktop window menu</li>
2267 <li>Visual indication that command line arguments are
2268 still being processed</li>
2269 <li>Groovy script execution from URL</li>
2270 <li>Colour by annotation default min and max colours in
2272 <li>Automatically associate PDB files dragged onto an
2273 alignment with sequences that have high similarity and
2275 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2276 <li>'view structures' option to open many
2277 structures in same window</li>
2278 <li>Sort associated views menu option for tree panel</li>
2279 <li>Group all JABA and non-JABA services for a particular
2280 analysis function in its own submenu</li>
2281 </ul> <em>Applet</em>
2283 <li>Userdefined and autogenerated annotation rows for
2285 <li>Adjustment of alignment annotation pane height</li>
2286 <li>Annotation scrollbar for annotation panel</li>
2287 <li>Drag to reorder annotation rows in annotation panel</li>
2288 <li>'automaticScrolling' parameter</li>
2289 <li>Allow sequences with partial ID string matches to be
2290 annotated from GFF/Jalview features files</li>
2291 <li>Sequence logo annotation row in applet</li>
2292 <li>Absolute paths relative to host server in applet
2293 parameters are treated as such</li>
2294 <li>New in the JalviewLite javascript API:
2296 <li>JalviewLite.js javascript library</li>
2297 <li>Javascript callbacks for
2299 <li>Applet initialisation</li>
2300 <li>Sequence/alignment mouse-overs and selections</li>
2303 <li>scrollTo row and column alignment scrolling
2305 <li>Select sequence/alignment regions from javascript</li>
2306 <li>javascript structure viewer harness to pass
2307 messages between Jmol and Jalview when running as
2308 distinct applets</li>
2309 <li>sortBy method</li>
2310 <li>Set of applet and application examples shipped
2311 with documentation</li>
2312 <li>New example to demonstrate JalviewLite and Jmol
2313 javascript message exchange</li>
2315 </ul> <em>General</em>
2317 <li>Enable Jmol displays to be associated with multiple
2318 multiple alignments</li>
2319 <li>Option to automatically sort alignment with new tree</li>
2320 <li>User configurable link to enable redirects to a
2321 www.Jalview.org mirror</li>
2322 <li>Jmol colours option for Jmol displays</li>
2323 <li>Configurable newline string when writing alignment
2324 and other flat files</li>
2325 <li>Allow alignment annotation description lines to
2326 contain html tags</li>
2327 </ul> <em>Documentation and Development</em>
2329 <li>Add groovy test harness for bulk load testing to
2331 <li>Groovy script to load and align a set of sequences
2332 using a web service before displaying the result in the
2333 Jalview desktop</li>
2334 <li>Restructured javascript and applet api documentation</li>
2335 <li>Ant target to publish example html files with applet
2337 <li>Netbeans project for building Jalview from source</li>
2338 <li>ant task to create online javadoc for Jalview source</li>
2340 <td><em>Application</em>
2342 <li>User defined colourscheme throws exception when
2343 current built in colourscheme is saved as new scheme</li>
2344 <li>AlignFrame->Save in application pops up save
2345 dialog for valid filename/format</li>
2346 <li>Cannot view associated structure for UniProt sequence</li>
2347 <li>PDB file association breaks for UniProt sequence
2349 <li>Associate PDB from file dialog does not tell you
2350 which sequence is to be associated with the file</li>
2351 <li>Find All raises null pointer exception when query
2352 only matches sequence IDs</li>
2353 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2354 <li>Jalview project with Jmol views created with Jalview
2355 2.4 cannot be loaded</li>
2356 <li>Filetype associations not installed for webstart
2358 <li>Two or more chains in a single PDB file associated
2359 with sequences in different alignments do not get coloured
2360 by their associated sequence</li>
2361 <li>Visibility status of autocalculated annotation row
2362 not preserved when project is loaded</li>
2363 <li>Annotation row height and visibility attributes not
2364 stored in Jalview project</li>
2365 <li>Tree bootstraps are not preserved when saved as a
2366 Jalview project</li>
2367 <li>Envision2 workflow tooltips are corrupted</li>
2368 <li>Enabling show group conservation also enables colour
2369 by conservation</li>
2370 <li>Duplicate group associated conservation or consensus
2371 created on new view</li>
2372 <li>Annotation scrollbar not displayed after 'show
2373 all hidden annotation rows' option selected</li>
2374 <li>Alignment quality not updated after alignment
2375 annotation row is hidden then shown</li>
2376 <li>Preserve colouring of structures coloured by
2377 sequences in pre Jalview 2.7 projects</li>
2378 <li>Web service job parameter dialog is not laid out
2380 <li>Web services menu not refreshed after 'reset
2381 services' button is pressed in preferences</li>
2382 <li>Annotation off by one in Jalview v2_3 example project</li>
2383 <li>Structures imported from file and saved in project
2384 get name like jalview_pdb1234.txt when reloaded</li>
2385 <li>Jalview does not always retrieve progress of a JABAWS
2386 job execution in full once it is complete</li>
2387 </ul> <em>Applet</em>
2389 <li>Alignment height set incorrectly when lots of
2390 annotation rows are displayed</li>
2391 <li>Relative URLs in feature HTML text not resolved to
2393 <li>View follows highlighting does not work for positions
2395 <li><= shown as = in tooltip</li>
2396 <li>Export features raises exception when no features
2398 <li>Separator string used for serialising lists of IDs
2399 for javascript api is modified when separator string
2400 provided as parameter</li>
2401 <li>Null pointer exception when selecting tree leaves for
2402 alignment with no existing selection</li>
2403 <li>Relative URLs for datasources assumed to be relative
2404 to applet's codebase</li>
2405 <li>Status bar not updated after finished searching and
2406 search wraps around to first result</li>
2407 <li>StructureSelectionManager instance shared between
2408 several Jalview applets causes race conditions and memory
2410 <li>Hover tooltip and mouseover of position on structure
2411 not sent from Jmol in applet</li>
2412 <li>Certain sequences of javascript method calls to
2413 applet API fatally hang browser</li>
2414 </ul> <em>General</em>
2416 <li>View follows structure mouseover scrolls beyond
2417 position with wrapped view and hidden regions</li>
2418 <li>Find sequence position moves to wrong residue
2419 with/without hidden columns</li>
2420 <li>Sequence length given in alignment properties window
2422 <li>InvalidNumberFormat exceptions thrown when trying to
2423 import PDB like structure files</li>
2424 <li>Positional search results are only highlighted
2425 between user-supplied sequence start/end bounds</li>
2426 <li>End attribute of sequence is not validated</li>
2427 <li>Find dialog only finds first sequence containing a
2428 given sequence position</li>
2429 <li>Sequence numbering not preserved in MSF alignment
2431 <li>Jalview PDB file reader does not extract sequence
2432 from nucleotide chains correctly</li>
2433 <li>Structure colours not updated when tree partition
2434 changed in alignment</li>
2435 <li>Sequence associated secondary structure not correctly
2436 parsed in interleaved stockholm</li>
2437 <li>Colour by annotation dialog does not restore current
2439 <li>Hiding (nearly) all sequences doesn't work
2441 <li>Sequences containing lowercase letters are not
2442 properly associated with their pdb files</li>
2443 </ul> <em>Documentation and Development</em>
2445 <li>schemas/JalviewWsParamSet.xsd corrupted by
2446 ApplyCopyright tool</li>
2451 <div align="center">
2452 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2455 <td><em>Application</em>
2457 <li>New warning dialog when the Jalview Desktop cannot
2458 contact web services</li>
2459 <li>JABA service parameters for a preset are shown in
2460 service job window</li>
2461 <li>JABA Service menu entries reworded</li>
2465 <li>Modeller PIR IO broken - cannot correctly import a
2466 pir file emitted by Jalview</li>
2467 <li>Existing feature settings transferred to new
2468 alignment view created from cut'n'paste</li>
2469 <li>Improved test for mixed amino/nucleotide chains when
2470 parsing PDB files</li>
2471 <li>Consensus and conservation annotation rows
2472 occasionally become blank for all new windows</li>
2473 <li>Exception raised when right clicking above sequences
2474 in wrapped view mode</li>
2475 </ul> <em>Application</em>
2477 <li>multiple multiply aligned structure views cause cpu
2478 usage to hit 100% and computer to hang</li>
2479 <li>Web Service parameter layout breaks for long user
2480 parameter names</li>
2481 <li>Jaba service discovery hangs desktop if Jaba server
2488 <div align="center">
2489 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2492 <td><em>Application</em>
2494 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2495 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2498 <li>Web Services preference tab</li>
2499 <li>Analysis parameters dialog box and user defined
2501 <li>Improved speed and layout of Envision2 service menu</li>
2502 <li>Superpose structures using associated sequence
2504 <li>Export coordinates and projection as CSV from PCA
2506 </ul> <em>Applet</em>
2508 <li>enable javascript: execution by the applet via the
2509 link out mechanism</li>
2510 </ul> <em>Other</em>
2512 <li>Updated the Jmol Jalview interface to work with Jmol
2514 <li>The Jalview Desktop and JalviewLite applet now
2515 require Java 1.5</li>
2516 <li>Allow Jalview feature colour specification for GFF
2517 sequence annotation files</li>
2518 <li>New 'colour by label' keword in Jalview feature file
2519 type colour specification</li>
2520 <li>New Jalview Desktop Groovy API method that allows a
2521 script to check if it being run in an interactive session or
2522 in a batch operation from the Jalview command line</li>
2526 <li>clustalx colourscheme colours Ds preferentially when
2527 both D+E are present in over 50% of the column</li>
2528 </ul> <em>Application</em>
2530 <li>typo in AlignmentFrame->View->Hide->all but
2531 selected Regions menu item</li>
2532 <li>sequence fetcher replaces ',' for ';' when the ',' is
2533 part of a valid accession ID</li>
2534 <li>fatal OOM if object retrieved by sequence fetcher
2535 runs out of memory</li>
2536 <li>unhandled Out of Memory Error when viewing pca
2537 analysis results</li>
2538 <li>InstallAnywhere builds fail to launch on OS X java
2539 10.5 update 4 (due to apple Java 1.6 update)</li>
2540 <li>Installanywhere Jalview silently fails to launch</li>
2541 </ul> <em>Applet</em>
2543 <li>Jalview.getFeatureGroups() raises an
2544 ArrayIndexOutOfBoundsException if no feature groups are
2551 <div align="center">
2552 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2558 <li>Alignment prettyprinter doesn't cope with long
2560 <li>clustalx colourscheme colours Ds preferentially when
2561 both D+E are present in over 50% of the column</li>
2562 <li>nucleic acid structures retrieved from PDB do not
2563 import correctly</li>
2564 <li>More columns get selected than were clicked on when a
2565 number of columns are hidden</li>
2566 <li>annotation label popup menu not providing correct
2567 add/hide/show options when rows are hidden or none are
2569 <li>Stockholm format shown in list of readable formats,
2570 and parser copes better with alignments from RFAM.</li>
2571 <li>CSV output of consensus only includes the percentage
2572 of all symbols if sequence logo display is enabled</li>
2574 </ul> <em>Applet</em>
2576 <li>annotation panel disappears when annotation is
2578 </ul> <em>Application</em>
2580 <li>Alignment view not redrawn properly when new
2581 alignment opened where annotation panel is visible but no
2582 annotations are present on alignment</li>
2583 <li>pasted region containing hidden columns is
2584 incorrectly displayed in new alignment window</li>
2585 <li>Jalview slow to complete operations when stdout is
2586 flooded (fix is to close the Jalview console)</li>
2587 <li>typo in AlignmentFrame->View->Hide->all but
2588 selected Rregions menu item.</li>
2589 <li>inconsistent group submenu and Format submenu entry
2590 'Un' or 'Non'conserved</li>
2591 <li>Sequence feature settings are being shared by
2592 multiple distinct alignments</li>
2593 <li>group annotation not recreated when tree partition is
2595 <li>double click on group annotation to select sequences
2596 does not propagate to associated trees</li>
2597 <li>Mac OSX specific issues:
2599 <li>exception raised when mouse clicked on desktop
2600 window background</li>
2601 <li>Desktop menu placed on menu bar and application
2602 name set correctly</li>
2603 <li>sequence feature settings not wide enough for the
2604 save feature colourscheme button</li>
2613 <div align="center">
2614 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2617 <td><em>New Capabilities</em>
2619 <li>URL links generated from description line for
2620 regular-expression based URL links (applet and application)
2622 <li>Non-positional feature URL links are shown in link
2624 <li>Linked viewing of nucleic acid sequences and
2626 <li>Automatic Scrolling option in View menu to display
2627 the currently highlighted region of an alignment.</li>
2628 <li>Order an alignment by sequence length, or using the
2629 average score or total feature count for each sequence.</li>
2630 <li>Shading features by score or associated description</li>
2631 <li>Subdivide alignment and groups based on identity of
2632 selected subsequence (Make Groups from Selection).</li>
2633 <li>New hide/show options including Shift+Control+H to
2634 hide everything but the currently selected region.</li>
2635 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2636 </ul> <em>Application</em>
2638 <li>Fetch DB References capabilities and UI expanded to
2639 support retrieval from DAS sequence sources</li>
2640 <li>Local DAS Sequence sources can be added via the
2641 command line or via the Add local source dialog box.</li>
2642 <li>DAS Dbref and DbxRef feature types are parsed as
2643 database references and protein_name is parsed as
2644 description line (BioSapiens terms).</li>
2645 <li>Enable or disable non-positional feature and database
2646 references in sequence ID tooltip from View menu in
2648 <!-- <li>New hidden columns and rows and representatives capabilities
2649 in annotations file (in progress - not yet fully implemented)</li> -->
2650 <li>Group-associated consensus, sequence logos and
2651 conservation plots</li>
2652 <li>Symbol distributions for each column can be exported
2653 and visualized as sequence logos</li>
2654 <li>Optionally scale multi-character column labels to fit
2655 within each column of annotation row<!-- todo for applet -->
2657 <li>Optional automatic sort of associated alignment view
2658 when a new tree is opened.</li>
2659 <li>Jalview Java Console</li>
2660 <li>Better placement of desktop window when moving
2661 between different screens.</li>
2662 <li>New preference items for sequence ID tooltip and
2663 consensus annotation</li>
2664 <li>Client to submit sequences and IDs to Envision2
2666 <li><em>Vamsas Capabilities</em>
2668 <li>Improved VAMSAS synchronization (Jalview archive
2669 used to preserve views, structures, and tree display
2671 <li>Import of vamsas documents from disk or URL via
2673 <li>Sharing of selected regions between views and
2674 with other VAMSAS applications (Experimental feature!)</li>
2675 <li>Updated API to VAMSAS version 0.2</li>
2677 </ul> <em>Applet</em>
2679 <li>Middle button resizes annotation row height</li>
2682 <li>sortByTree (true/false) - automatically sort the
2683 associated alignment view by the tree when a new tree is
2685 <li>showTreeBootstraps (true/false) - show or hide
2686 branch bootstraps (default is to show them if available)</li>
2687 <li>showTreeDistances (true/false) - show or hide
2688 branch lengths (default is to show them if available)</li>
2689 <li>showUnlinkedTreeNodes (true/false) - indicate if
2690 unassociated nodes should be highlighted in the tree
2692 <li>heightScale and widthScale (1.0 or more) -
2693 increase the height or width of a cell in the alignment
2694 grid relative to the current font size.</li>
2697 <li>Non-positional features displayed in sequence ID
2699 </ul> <em>Other</em>
2701 <li>Features format: graduated colour definitions and
2702 specification of feature scores</li>
2703 <li>Alignment Annotations format: new keywords for group
2704 associated annotation (GROUP_REF) and annotation row display
2705 properties (ROW_PROPERTIES)</li>
2706 <li>XML formats extended to support graduated feature
2707 colourschemes, group associated annotation, and profile
2708 visualization settings.</li></td>
2711 <li>Source field in GFF files parsed as feature source
2712 rather than description</li>
2713 <li>Non-positional features are now included in sequence
2714 feature and gff files (controlled via non-positional feature
2715 visibility in tooltip).</li>
2716 <li>URL links generated for all feature links (bugfix)</li>
2717 <li>Added URL embedding instructions to features file
2719 <li>Codons containing ambiguous nucleotides translated as
2720 'X' in peptide product</li>
2721 <li>Match case switch in find dialog box works for both
2722 sequence ID and sequence string and query strings do not
2723 have to be in upper case to match case-insensitively.</li>
2724 <li>AMSA files only contain first column of
2725 multi-character column annotation labels</li>
2726 <li>Jalview Annotation File generation/parsing consistent
2727 with documentation (e.g. Stockholm annotation can be
2728 exported and re-imported)</li>
2729 <li>PDB files without embedded PDB IDs given a friendly
2731 <li>Find incrementally searches ID string matches as well
2732 as subsequence matches, and correctly reports total number
2736 <li>Better handling of exceptions during sequence
2738 <li>Dasobert generated non-positional feature URL
2739 link text excludes the start_end suffix</li>
2740 <li>DAS feature and source retrieval buttons disabled
2741 when fetch or registry operations in progress.</li>
2742 <li>PDB files retrieved from URLs are cached properly</li>
2743 <li>Sequence description lines properly shared via
2745 <li>Sequence fetcher fetches multiple records for all
2747 <li>Ensured that command line das feature retrieval
2748 completes before alignment figures are generated.</li>
2749 <li>Reduced time taken when opening file browser for
2751 <li>isAligned check prior to calculating tree, PCA or
2752 submitting an MSA to JNet now excludes hidden sequences.</li>
2753 <li>User defined group colours properly recovered
2754 from Jalview projects.</li>
2763 <div align="center">
2764 <strong>2.4.0.b2</strong><br> 28/10/2009
2769 <li>Experimental support for google analytics usage
2771 <li>Jalview privacy settings (user preferences and docs).</li>
2776 <li>Race condition in applet preventing startup in
2778 <li>Exception when feature created from selection beyond
2779 length of sequence.</li>
2780 <li>Allow synthetic PDB files to be imported gracefully</li>
2781 <li>Sequence associated annotation rows associate with
2782 all sequences with a given id</li>
2783 <li>Find function matches case-insensitively for sequence
2784 ID string searches</li>
2785 <li>Non-standard characters do not cause pairwise
2786 alignment to fail with exception</li>
2787 </ul> <em>Application Issues</em>
2789 <li>Sequences are now validated against EMBL database</li>
2790 <li>Sequence fetcher fetches multiple records for all
2792 </ul> <em>InstallAnywhere Issues</em>
2794 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2795 issue with installAnywhere mechanism)</li>
2796 <li>Command line launching of JARs from InstallAnywhere
2797 version (java class versioning error fixed)</li>
2804 <div align="center">
2805 <strong>2.4</strong><br> 27/8/2008
2808 <td><em>User Interface</em>
2810 <li>Linked highlighting of codon and amino acid from
2811 translation and protein products</li>
2812 <li>Linked highlighting of structure associated with
2813 residue mapping to codon position</li>
2814 <li>Sequence Fetcher provides example accession numbers
2815 and 'clear' button</li>
2816 <li>MemoryMonitor added as an option under Desktop's
2818 <li>Extract score function to parse whitespace separated
2819 numeric data in description line</li>
2820 <li>Column labels in alignment annotation can be centred.</li>
2821 <li>Tooltip for sequence associated annotation give name
2823 </ul> <em>Web Services and URL fetching</em>
2825 <li>JPred3 web service</li>
2826 <li>Prototype sequence search client (no public services
2828 <li>Fetch either seed alignment or full alignment from
2830 <li>URL Links created for matching database cross
2831 references as well as sequence ID</li>
2832 <li>URL Links can be created using regular-expressions</li>
2833 </ul> <em>Sequence Database Connectivity</em>
2835 <li>Retrieval of cross-referenced sequences from other
2837 <li>Generalised database reference retrieval and
2838 validation to all fetchable databases</li>
2839 <li>Fetch sequences from DAS sources supporting the
2840 sequence command</li>
2841 </ul> <em>Import and Export</em>
2842 <li>export annotation rows as CSV for spreadsheet import</li>
2843 <li>Jalview projects record alignment dataset associations,
2844 EMBL products, and cDNA sequence mappings</li>
2845 <li>Sequence Group colour can be specified in Annotation
2847 <li>Ad-hoc colouring of group in Annotation File using RGB
2848 triplet as name of colourscheme</li>
2849 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2851 <li>treenode binding for VAMSAS tree exchange</li>
2852 <li>local editing and update of sequences in VAMSAS
2853 alignments (experimental)</li>
2854 <li>Create new or select existing session to join</li>
2855 <li>load and save of vamsas documents</li>
2856 </ul> <em>Application command line</em>
2858 <li>-tree parameter to open trees (introduced for passing
2860 <li>-fetchfrom command line argument to specify nicknames
2861 of DAS servers to query for alignment features</li>
2862 <li>-dasserver command line argument to add new servers
2863 that are also automatically queried for features</li>
2864 <li>-groovy command line argument executes a given groovy
2865 script after all input data has been loaded and parsed</li>
2866 </ul> <em>Applet-Application data exchange</em>
2868 <li>Trees passed as applet parameters can be passed to
2869 application (when using "View in full
2870 application")</li>
2871 </ul> <em>Applet Parameters</em>
2873 <li>feature group display control parameter</li>
2874 <li>debug parameter</li>
2875 <li>showbutton parameter</li>
2876 </ul> <em>Applet API methods</em>
2878 <li>newView public method</li>
2879 <li>Window (current view) specific get/set public methods</li>
2880 <li>Feature display control methods</li>
2881 <li>get list of currently selected sequences</li>
2882 </ul> <em>New Jalview distribution features</em>
2884 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2885 <li>RELEASE file gives build properties for the latest
2886 Jalview release.</li>
2887 <li>Java 1.1 Applet build made easier and donotobfuscate
2888 property controls execution of obfuscator</li>
2889 <li>Build target for generating source distribution</li>
2890 <li>Debug flag for javacc</li>
2891 <li>.jalview_properties file is documented (slightly) in
2892 jalview.bin.Cache</li>
2893 <li>Continuous Build Integration for stable and
2894 development version of Application, Applet and source
2899 <li>selected region output includes visible annotations
2900 (for certain formats)</li>
2901 <li>edit label/displaychar contains existing label/char
2903 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2904 <li>shorter peptide product names from EMBL records</li>
2905 <li>Newick string generator makes compact representations</li>
2906 <li>bootstrap values parsed correctly for tree files with
2908 <li>pathological filechooser bug avoided by not allowing
2909 filenames containing a ':'</li>
2910 <li>Fixed exception when parsing GFF files containing
2911 global sequence features</li>
2912 <li>Alignment datasets are finalized only when number of
2913 references from alignment sequences goes to zero</li>
2914 <li>Close of tree branch colour box without colour
2915 selection causes cascading exceptions</li>
2916 <li>occasional negative imgwidth exceptions</li>
2917 <li>better reporting of non-fatal warnings to user when
2918 file parsing fails.</li>
2919 <li>Save works when Jalview project is default format</li>
2920 <li>Save as dialog opened if current alignment format is
2921 not a valid output format</li>
2922 <li>UniProt canonical names introduced for both das and
2924 <li>Histidine should be midblue (not pink!) in Zappo</li>
2925 <li>error messages passed up and output when data read
2927 <li>edit undo recovers previous dataset sequence when
2928 sequence is edited</li>
2929 <li>allow PDB files without pdb ID HEADER lines (like
2930 those generated by MODELLER) to be read in properly</li>
2931 <li>allow reading of JPred concise files as a normal
2933 <li>Stockholm annotation parsing and alignment properties
2934 import fixed for PFAM records</li>
2935 <li>Structure view windows have correct name in Desktop
2937 <li>annotation consisting of sequence associated scores
2938 can be read and written correctly to annotation file</li>
2939 <li>Aligned cDNA translation to aligned peptide works
2941 <li>Fixed display of hidden sequence markers and
2942 non-italic font for representatives in Applet</li>
2943 <li>Applet Menus are always embedded in applet window on
2945 <li>Newly shown features appear at top of stack (in
2947 <li>Annotations added via parameter not drawn properly
2948 due to null pointer exceptions</li>
2949 <li>Secondary structure lines are drawn starting from
2950 first column of alignment</li>
2951 <li>UniProt XML import updated for new schema release in
2953 <li>Sequence feature to sequence ID match for Features
2954 file is case-insensitive</li>
2955 <li>Sequence features read from Features file appended to
2956 all sequences with matching IDs</li>
2957 <li>PDB structure coloured correctly for associated views
2958 containing a sub-sequence</li>
2959 <li>PDB files can be retrieved by applet from Jar files</li>
2960 <li>feature and annotation file applet parameters
2961 referring to different directories are retrieved correctly</li>
2962 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2963 <li>Fixed application hang whilst waiting for
2964 splash-screen version check to complete</li>
2965 <li>Applet properly URLencodes input parameter values
2966 when passing them to the launchApp service</li>
2967 <li>display name and local features preserved in results
2968 retrieved from web service</li>
2969 <li>Visual delay indication for sequence retrieval and
2970 sequence fetcher initialisation</li>
2971 <li>updated Application to use DAS 1.53e version of
2972 dasobert DAS client</li>
2973 <li>Re-instated Full AMSA support and .amsa file
2975 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2983 <div align="center">
2984 <strong>2.3</strong><br> 9/5/07
2989 <li>Jmol 11.0.2 integration</li>
2990 <li>PDB views stored in Jalview XML files</li>
2991 <li>Slide sequences</li>
2992 <li>Edit sequence in place</li>
2993 <li>EMBL CDS features</li>
2994 <li>DAS Feature mapping</li>
2995 <li>Feature ordering</li>
2996 <li>Alignment Properties</li>
2997 <li>Annotation Scores</li>
2998 <li>Sort by scores</li>
2999 <li>Feature/annotation editing in applet</li>
3004 <li>Headless state operation in 2.2.1</li>
3005 <li>Incorrect and unstable DNA pairwise alignment</li>
3006 <li>Cut and paste of sequences with annotation</li>
3007 <li>Feature group display state in XML</li>
3008 <li>Feature ordering in XML</li>
3009 <li>blc file iteration selection using filename # suffix</li>
3010 <li>Stockholm alignment properties</li>
3011 <li>Stockhom alignment secondary structure annotation</li>
3012 <li>2.2.1 applet had no feature transparency</li>
3013 <li>Number pad keys can be used in cursor mode</li>
3014 <li>Structure Viewer mirror image resolved</li>
3021 <div align="center">
3022 <strong>2.2.1</strong><br> 12/2/07
3027 <li>Non standard characters can be read and displayed
3028 <li>Annotations/Features can be imported/exported to the
3030 <li>Applet allows editing of sequence/annotation/group
3031 name & description
3032 <li>Preference setting to display sequence name in
3034 <li>Annotation file format extended to allow
3035 Sequence_groups to be defined
3036 <li>Default opening of alignment overview panel can be
3037 specified in preferences
3038 <li>PDB residue numbering annotation added to associated
3044 <li>Applet crash under certain Linux OS with Java 1.6
3046 <li>Annotation file export / import bugs fixed
3047 <li>PNG / EPS image output bugs fixed
3053 <div align="center">
3054 <strong>2.2</strong><br> 27/11/06
3059 <li>Multiple views on alignment
3060 <li>Sequence feature editing
3061 <li>"Reload" alignment
3062 <li>"Save" to current filename
3063 <li>Background dependent text colour
3064 <li>Right align sequence ids
3065 <li>User-defined lower case residue colours
3068 <li>Menu item accelerator keys
3069 <li>Control-V pastes to current alignment
3070 <li>Cancel button for DAS Feature Fetching
3071 <li>PCA and PDB Viewers zoom via mouse roller
3072 <li>User-defined sub-tree colours and sub-tree selection
3074 <li>'New Window' button on the 'Output to Text box'
3079 <li>New memory efficient Undo/Redo System
3080 <li>Optimised symbol lookups and conservation/consensus
3082 <li>Region Conservation/Consensus recalculated after
3084 <li>Fixed Remove Empty Columns Bug (empty columns at end
3086 <li>Slowed DAS Feature Fetching for increased robustness.
3088 <li>Made angle brackets in ASCII feature descriptions
3090 <li>Re-instated Zoom function for PCA
3091 <li>Sequence descriptions conserved in web service
3093 <li>UniProt ID discoverer uses any word separated by
3095 <li>WsDbFetch query/result association resolved
3096 <li>Tree leaf to sequence mapping improved
3097 <li>Smooth fonts switch moved to FontChooser dialog box.
3104 <div align="center">
3105 <strong>2.1.1</strong><br> 12/9/06
3110 <li>Copy consensus sequence to clipboard</li>
3115 <li>Image output - rightmost residues are rendered if
3116 sequence id panel has been resized</li>
3117 <li>Image output - all offscreen group boundaries are
3119 <li>Annotation files with sequence references - all
3120 elements in file are relative to sequence position</li>
3121 <li>Mac Applet users can use Alt key for group editing</li>
3127 <div align="center">
3128 <strong>2.1</strong><br> 22/8/06
3133 <li>MAFFT Multiple Alignment in default Web Service list</li>
3134 <li>DAS Feature fetching</li>
3135 <li>Hide sequences and columns</li>
3136 <li>Export Annotations and Features</li>
3137 <li>GFF file reading / writing</li>
3138 <li>Associate structures with sequences from local PDB
3140 <li>Add sequences to exisiting alignment</li>
3141 <li>Recently opened files / URL lists</li>
3142 <li>Applet can launch the full application</li>
3143 <li>Applet has transparency for features (Java 1.2
3145 <li>Applet has user defined colours parameter</li>
3146 <li>Applet can load sequences from parameter
3147 "sequence<em>x</em>"
3153 <li>Redundancy Panel reinstalled in the Applet</li>
3154 <li>Monospaced font - EPS / rescaling bug fixed</li>
3155 <li>Annotation files with sequence references bug fixed</li>
3161 <div align="center">
3162 <strong>2.08.1</strong><br> 2/5/06
3167 <li>Change case of selected region from Popup menu</li>
3168 <li>Choose to match case when searching</li>
3169 <li>Middle mouse button and mouse movement can compress /
3170 expand the visible width and height of the alignment</li>
3175 <li>Annotation Panel displays complete JNet results</li>
3181 <div align="center">
3182 <strong>2.08b</strong><br> 18/4/06
3188 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3189 <li>Righthand label on wrapped alignments shows correct
3196 <div align="center">
3197 <strong>2.08</strong><br> 10/4/06
3202 <li>Editing can be locked to the selection area</li>
3203 <li>Keyboard editing</li>
3204 <li>Create sequence features from searches</li>
3205 <li>Precalculated annotations can be loaded onto
3207 <li>Features file allows grouping of features</li>
3208 <li>Annotation Colouring scheme added</li>
3209 <li>Smooth fonts off by default - Faster rendering</li>
3210 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3215 <li>Drag & Drop fixed on Linux</li>
3216 <li>Jalview Archive file faster to load/save, sequence
3217 descriptions saved.</li>
3223 <div align="center">
3224 <strong>2.07</strong><br> 12/12/05
3229 <li>PDB Structure Viewer enhanced</li>
3230 <li>Sequence Feature retrieval and display enhanced</li>
3231 <li>Choose to output sequence start-end after sequence
3232 name for file output</li>
3233 <li>Sequence Fetcher WSDBFetch@EBI</li>
3234 <li>Applet can read feature files, PDB files and can be
3235 used for HTML form input</li>
3240 <li>HTML output writes groups and features</li>
3241 <li>Group editing is Control and mouse click</li>
3242 <li>File IO bugs</li>
3248 <div align="center">
3249 <strong>2.06</strong><br> 28/9/05
3254 <li>View annotations in wrapped mode</li>
3255 <li>More options for PCA viewer</li>
3260 <li>GUI bugs resolved</li>
3261 <li>Runs with -nodisplay from command line</li>
3267 <div align="center">
3268 <strong>2.05b</strong><br> 15/9/05
3273 <li>Choose EPS export as lineart or text</li>
3274 <li>Jar files are executable</li>
3275 <li>Can read in Uracil - maps to unknown residue</li>
3280 <li>Known OutOfMemory errors give warning message</li>
3281 <li>Overview window calculated more efficiently</li>
3282 <li>Several GUI bugs resolved</li>
3288 <div align="center">
3289 <strong>2.05</strong><br> 30/8/05
3294 <li>Edit and annotate in "Wrapped" view</li>
3299 <li>Several GUI bugs resolved</li>
3305 <div align="center">
3306 <strong>2.04</strong><br> 24/8/05
3311 <li>Hold down mouse wheel & scroll to change font
3317 <li>Improved JPred client reliability</li>
3318 <li>Improved loading of Jalview files</li>
3324 <div align="center">
3325 <strong>2.03</strong><br> 18/8/05
3330 <li>Set Proxy server name and port in preferences</li>
3331 <li>Multiple URL links from sequence ids</li>
3332 <li>User Defined Colours can have a scheme name and added
3334 <li>Choose to ignore gaps in consensus calculation</li>
3335 <li>Unix users can set default web browser</li>
3336 <li>Runs without GUI for batch processing</li>
3337 <li>Dynamically generated Web Service Menus</li>
3342 <li>InstallAnywhere download for Sparc Solaris</li>
3348 <div align="center">
3349 <strong>2.02</strong><br> 18/7/05
3355 <li>Copy & Paste order of sequences maintains
3356 alignment order.</li>
3362 <div align="center">
3363 <strong>2.01</strong><br> 12/7/05
3368 <li>Use delete key for deleting selection.</li>
3369 <li>Use Mouse wheel to scroll sequences.</li>
3370 <li>Help file updated to describe how to add alignment
3372 <li>Version and build date written to build properties
3374 <li>InstallAnywhere installation will check for updates
3375 at launch of Jalview.</li>
3380 <li>Delete gaps bug fixed.</li>
3381 <li>FileChooser sorts columns.</li>
3382 <li>Can remove groups one by one.</li>
3383 <li>Filechooser icons installed.</li>
3384 <li>Finder ignores return character when searching.
3385 Return key will initiate a search.<br>
3392 <div align="center">
3393 <strong>2.0</strong><br> 20/6/05
3398 <li>New codebase</li>