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.2.10.2b1">2.10.2b1</a><br />
77 <td><div align="left">
81 <!-- JAL-2588 -->Show gaps in overview window by colouring
82 in grey (sequences used to be coloured grey, and gaps were
85 <li><!-- JAL-2588 -->Overview tab in Jalview Desktop Preferences</li>
88 <td><div align="left">
92 <!-- JAL-2681 -->duplicate protein sequences shown after
93 retrieving Ensembl crossrefs for sequences from Uniprot
95 <li> <!-- JAL-2603 -->Overview window throws NPE if show boxes
96 format setting is unticked
99 <!-- JAL-2610 -->Groups are coloured wrongly in overview
100 if group has show boxes format setting unticked
106 <td width="60" nowrap>
108 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
111 <td><div align="left">
112 <em>Calculations</em>
116 <!-- JAL-1933 -->Occupancy annotation row shows number of
117 ungapped positions in each column of the alignment.
120 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
121 a calculation dialog box
124 <!-- JAL-2379 -->Revised implementation of PCA for speed
125 and memory efficiency (~30x faster)
128 <!-- JAL-2403 -->Revised implementation of sequence
129 similarity scores as used by Tree, PCA, Shading Consensus
130 and other calculations
133 <!-- JAL-2416 -->Score matrices are stored as resource
134 files within the Jalview codebase
137 <!-- JAL-2500 -->Trees computed on Sequence Feature
138 Similarity may have different topology due to increased
145 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
146 model for alignments and groups
149 <!-- JAL-384 -->Custom shading schemes created via groovy
156 <!-- JAL-2526 -->Efficiency improvements for interacting
157 with alignment and overview windows
160 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
164 <!-- JAL-2388 -->Hidden columns and sequences can be
168 <!-- JAL-2611 -->Click-drag in visible area allows fine
169 adjustment of visible position
173 <em>Data import/export</em>
176 <!-- JAL-2535 -->Posterior probability annotation from
177 Stockholm files imported as sequence associated annotation
180 <!-- JAL-2507 -->More robust per-sequence positional
181 annotation input/output via stockholm flatfile
184 <!-- JAL-2533 -->Sequence names don't include file
185 extension when importing structure files without embedded
186 names or PDB accessions
189 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
190 format sequence substitution matrices
193 <em>User Interface</em>
196 <!-- JAL-2447 --> Experimental Features Checkbox in
197 Desktop's Tools menu to hide or show untested features in
201 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
202 via Overview or sequence motif search operations
205 <!-- JAL-2547 -->Amend sequence features dialog box can be
206 opened by double clicking gaps within sequence feature
210 <!-- JAL-1476 -->Status bar message shown when not enough
211 aligned positions were available to create a 3D structure
215 <em>3D Structure</em>
218 <!-- JAL-2430 -->Hidden regions in alignment views are not
219 coloured in linked structure views
222 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
223 file-based command exchange
226 <!-- JAL-2375 -->Structure chooser automatically shows
227 Cached Structures rather than querying the PDBe if
228 structures are already available for sequences
231 <!-- JAL-2520 -->Structures imported via URL are cached in
232 the Jalview project rather than downloaded again when the
236 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
237 to transfer Chimera's structure attributes as Jalview
238 features, and vice-versa (<strong>Experimental
242 <em>Web Services</em>
245 <!-- JAL-2549 -->Updated JABAWS client to v2.2
248 <!-- JAL-2335 -->Filter non-standard amino acids and
249 nucleotides when submitting to AACon and other MSA
253 <!-- JAL-2316, -->URLs for viewing database
254 cross-references provided by identifiers.org and the
262 <!-- JAL-2344 -->FileFormatI interface for describing and
263 identifying file formats (instead of String constants)
266 <!-- JAL-2228 -->FeatureCounter script refactored for
267 efficiency when counting all displayed features (not
268 backwards compatible with 2.10.1)
271 <em>Example files</em>
274 <!-- JAL-2631 -->Graduated feature colour style example
275 included in the example feature file
278 <em>Documentation</em>
281 <!-- JAL-2339 -->Release notes reformatted for readability
282 with the built-in Java help viewer
285 <!-- JAL-1644 -->Find documentation updated with 'search
286 sequence description' option
292 <!-- JAL-2485, -->External service integration tests for
293 Uniprot REST Free Text Search Client
296 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
299 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
304 <td><div align="left">
305 <em>Calculations</em>
308 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
309 matrix - C->R should be '-3'<br />Old matrix restored
310 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
312 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
313 Jalview's treatment of gaps in PCA and substitution matrix
314 based Tree calculations.<br /> <br />In earlier versions
315 of Jalview, gaps matching gaps were penalised, and gaps
316 matching non-gaps penalised even more. In the PCA
317 calculation, gaps were actually treated as non-gaps - so
318 different costs were applied, which meant Jalview's PCAs
319 were different to those produced by SeqSpace.<br />Jalview
320 now treats gaps in the same way as SeqSpace (ie it scores
321 them as 0). <br /> <br />Enter the following in the
322 Groovy console to restore pre-2.10.2 behaviour:<br />
323 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
324 // for 2.10.1 mode <br />
325 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
326 // to restore 2.10.2 mode <br /> <br /> <em>Note:
327 these settings will affect all subsequent tree and PCA
328 calculations (not recommended)</em></li>
330 <!-- JAL-2424 -->Fixed off-by-one bug that affected
331 scaling of branch lengths for trees computed using
332 Sequence Feature Similarity.
335 <!-- JAL-2377 -->PCA calculation could hang when
336 generating output report when working with highly
340 <!-- JAL-2544 --> Sort by features includes features to
341 right of selected region when gaps present on right-hand
345 <em>User Interface</em>
348 <!-- JAL-2346 -->Reopening Colour by annotation dialog
349 doesn't reselect a specific sequence's associated
350 annotation after it was used for colouring a view
353 <!-- JAL-2419 -->Current selection lost if popup menu
354 opened on a region of alignment without groups
357 <!-- JAL-2374 -->Popup menu not always shown for regions
358 of an alignment with overlapping groups
361 <!-- JAL-2310 -->Finder double counts if both a sequence's
362 name and description match
365 <!-- JAL-2370 -->Hiding column selection containing two
366 hidden regions results in incorrect hidden regions
369 <!-- JAL-2386 -->'Apply to all groups' setting when
370 changing colour does not apply Conservation slider value
374 <!-- JAL-2373 -->Percentage identity and conservation menu
375 items do not show a tick or allow shading to be disabled
378 <!-- JAL-2385 -->Conservation shading or PID threshold
379 lost when base colourscheme changed if slider not visible
382 <!-- JAL-2547 -->Sequence features shown in tooltip for
383 gaps before start of features
386 <!-- JAL-2623 -->Graduated feature colour threshold not
387 restored to UI when feature colour is edited
390 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
391 a time when scrolling vertically in wrapped mode.
394 <!-- JAL-2630 -->Structure and alignment overview update
395 as graduate feature colour settings are modified via the
399 <!-- JAL-2034 -->Overview window doesn't always update
400 when a group defined on the alignment is resized
403 <!-- JAL-2605 -->Mouseovers on left/right scale region in
404 wrapped view result in positional status updates
408 <!-- JAL-2563 -->Status bar doesn't show position for
409 ambiguous amino acid and nucleotide symbols
412 <!-- JAL-2602 -->Copy consensus sequence failed if
413 alignment included gapped columns
416 <!-- JAL-2473 -->Minimum size set for Jalview windows so
417 widgets don't permanently disappear
420 <!-- JAL-2503 -->Cannot select or filter quantitative
421 annotation that are shown only as column labels (e.g.
422 T-Coffee column reliability scores)
425 <!-- JAL-2594 -->Exception thrown if trying to create a
426 sequence feature on gaps only
429 <!-- JAL-2504 -->Features created with 'New feature'
430 button from a Find inherit previously defined feature type
431 rather than the Find query string
434 <!-- JAL-2423 -->incorrect title in output window when
435 exporting tree calculated in Jalview
438 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
439 and then revealing them reorders sequences on the
443 <!-- JAL-964 -->Group panel in sequence feature settings
444 doesn't update to reflect available set of groups after
445 interactively adding or modifying features
448 <!-- JAL-2225 -->Sequence Database chooser unusable on
452 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
453 only excluded gaps in current sequence and ignored
460 <!-- JAL-2421 -->Overview window visible region moves
461 erratically when hidden rows or columns are present
464 <!-- JAL-2362 -->Per-residue colourschemes applied via the
465 Structure Viewer's colour menu don't correspond to
469 <!-- JAL-2405 -->Protein specific colours only offered in
470 colour and group colour menu for protein alignments
473 <!-- JAL-2385 -->Colour threshold slider doesn't update to
474 reflect currently selected view or group's shading
478 <!-- JAL-2624 -->Feature colour thresholds not respected
479 when rendered on overview and structures when opacity at
483 <!-- JAL-2589 -->User defined gap colour not shown in
484 overview when features overlaid on alignment
487 <em>Data import/export</em>
490 <!-- JAL-2576 -->Very large alignments take a long time to
494 <!-- JAL-2507 -->Per-sequence RNA secondary structures
495 added after a sequence was imported are not written to
499 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
500 when importing RNA secondary structure via Stockholm
503 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
504 not shown in correct direction for simple pseudoknots
507 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
508 with lightGray or darkGray via features file (but can
512 <!-- JAL-2383 -->Above PID colour threshold not recovered
513 when alignment view imported from project
516 <!-- JAL-2520,JAL-2465 -->No mappings generated between
517 structure and sequences extracted from structure files
518 imported via URL and viewed in Jmol
521 <!-- JAL-2520 -->Structures loaded via URL are saved in
522 Jalview Projects rather than fetched via URL again when
523 the project is loaded and the structure viewed
526 <em>Web Services</em>
529 <!-- JAL-2519 -->EnsemblGenomes example failing after
530 release of Ensembl v.88
533 <!-- JAL-2366 -->Proxy server address and port always
534 appear enabled in Preferences->Connections
537 <!-- JAL-2461 -->DAS registry not found exceptions
538 removed from console output
541 <!-- JAL-2582 -->Cannot retrieve protein products from
542 Ensembl by Peptide ID
545 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
546 created from SIFTs, and spurious 'Couldn't open structure
547 in Chimera' errors raised after April 2017 update (problem
548 due to 'null' string rather than empty string used for
549 residues with no corresponding PDB mapping).
552 <em>Application UI</em>
555 <!-- JAL-2361 -->User Defined Colours not added to Colour
559 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
560 case' residues (button in colourscheme editor debugged and
561 new documentation and tooltips added)
564 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
565 doesn't restore group-specific text colour thresholds
568 <!-- JAL-2243 -->Feature settings panel does not update as
569 new features are added to alignment
572 <!-- JAL-2532 -->Cancel in feature settings reverts
573 changes to feature colours via the Amend features dialog
576 <!-- JAL-2506 -->Null pointer exception when attempting to
577 edit graduated feature colour via amend features dialog
581 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
582 selection menu changes colours of alignment views
585 <!-- JAL-2426 -->Spurious exceptions in console raised
586 from alignment calculation workers after alignment has
590 <!-- JAL-1608 -->Typo in selection popup menu - Create
591 groups now 'Create Group'
594 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
595 Create/Undefine group doesn't always work
598 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
599 shown again after pressing 'Cancel'
602 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
603 adjusts start position in wrap mode
606 <!-- JAL-2563 -->Status bar doesn't show positions for
607 ambiguous amino acids
610 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
611 CDS/Protein view after CDS sequences added for aligned
615 <!-- JAL-2592 -->User defined colourschemes called 'User
616 Defined' don't appear in Colours menu
622 <!-- JAL-2468 -->Switching between Nucleotide and Protein
623 score models doesn't always result in an updated PCA plot
626 <!-- JAL-2442 -->Features not rendered as transparent on
627 overview or linked structure view
630 <!-- JAL-2372 -->Colour group by conservation doesn't
634 <!-- JAL-2517 -->Hitting Cancel after applying
635 user-defined colourscheme doesn't restore original
642 <!-- JAL-2314 -->Unit test failure:
643 jalview.ws.jabaws.RNAStructExportImport setup fails
646 <!-- JAL-2307 -->Unit test failure:
647 jalview.ws.sifts.SiftsClientTest due to compatibility
648 problems with deep array comparison equality asserts in
649 successive versions of TestNG
652 <!-- JAL-2479 -->Relocated StructureChooserTest and
653 ParameterUtilsTest Unit tests to Network suite
656 <em>New Known Issues</em>
659 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
660 phase after a sequence motif find operation
663 <!-- JAL-2550 -->Importing annotation file with rows
664 containing just upper and lower case letters are
665 interpreted as WUSS RNA secondary structure symbols
668 <!-- JAL-2590 -->Cannot load and display Newick trees
669 reliably from eggnog Ortholog database
672 <!-- JAL-2468 -->Status bar shows 'Marked x columns
673 containing features of type Highlight' when 'B' is pressed
674 to mark columns containing highlighted regions.
677 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
678 doesn't always add secondary structure annotation.
683 <td width="60" nowrap>
685 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
688 <td><div align="left">
692 <!-- JAL-98 -->Improved memory usage: sparse arrays used
693 for all consensus calculations
696 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
699 <li>Updated Jalview's Certum code signing certificate
705 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
706 set of database cross-references, sorted alphabetically
709 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
710 from database cross references. Users with custom links
711 will receive a <a href="webServices/urllinks.html#warning">warning
712 dialog</a> asking them to update their preferences.
715 <!-- JAL-2287-->Cancel button and escape listener on
716 dialog warning user about disconnecting Jalview from a
720 <!-- JAL-2320-->Jalview's Chimera control window closes if
721 the Chimera it is connected to is shut down
724 <!-- JAL-1738-->New keystroke (B) and Select highlighted
725 columns menu item to mark columns containing highlighted
726 regions (e.g. from structure selections or results of a
730 <!-- JAL-2284-->Command line option for batch-generation
731 of HTML pages rendering alignment data with the BioJS
741 <!-- JAL-2286 -->Columns with more than one modal residue
742 are not coloured or thresholded according to percent
743 identity (first observed in Jalview 2.8.2)
746 <!-- JAL-2301 -->Threonine incorrectly reported as not
750 <!-- JAL-2318 -->Updates to documentation pages (above PID
751 threshold, amino acid properties)
754 <!-- JAL-2292 -->Lower case residues in sequences are not
755 reported as mapped to residues in a structure file in the
759 <!--JAL-2324 -->Identical features with non-numeric scores
760 could be added multiple times to a sequence
763 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
764 bond features shown as two highlighted residues rather
765 than a range in linked structure views, and treated
766 correctly when selecting and computing trees from features
769 <!-- JAL-2281-->Custom URL links for database
770 cross-references are matched to database name regardless
778 <!-- JAL-2282-->Custom URL links for specific database
779 names without regular expressions also offer links from
783 <!-- JAL-2315-->Removing a single configured link in the
784 URL links pane in Connections preferences doesn't actually
785 update Jalview configuration
788 <!-- JAL-2272-->CTRL-Click on a selected region to open
789 the alignment area popup menu doesn't work on El-Capitan
792 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
793 files with similarly named sequences if dropped onto the
797 <!-- JAL-2312 -->Additional mappings are shown for PDB
798 entries where more chains exist in the PDB accession than
799 are reported in the SIFTS file
802 <!-- JAL-2317-->Certain structures do not get mapped to
803 the structure view when displayed with Chimera
806 <!-- JAL-2317-->No chains shown in the Chimera view
807 panel's View->Show Chains submenu
810 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
811 work for wrapped alignment views
814 <!--JAL-2197 -->Rename UI components for running JPred
815 predictions from 'JNet' to 'JPred'
818 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
819 corrupted when annotation panel vertical scroll is not at
823 <!--JAL-2332 -->Attempting to view structure for Hen
824 lysozyme results in a PDB Client error dialog box
827 <!-- JAL-2319 -->Structure View's mapping report switched
828 ranges for PDB and sequence for SIFTS
831 SIFTS 'Not_Observed' residues mapped to non-existant
835 <!-- <em>New Known Issues</em>
842 <td width="60" nowrap>
844 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
845 <em>25/10/2016</em></strong>
848 <td><em>Application</em>
850 <li>3D Structure chooser opens with 'Cached structures'
851 view if structures already loaded</li>
852 <li>Progress bar reports models as they are loaded to
859 <li>Colour by conservation always enabled and no tick
860 shown in menu when BLOSUM or PID shading applied</li>
861 <li>FER1_ARATH and FER2_ARATH labels were switched in
862 example sequences/projects/trees</li>
866 <li>Jalview projects with views of local PDB structure
867 files saved on Windows cannot be opened on OSX</li>
868 <li>Multiple structure views can be opened and superposed
869 without timeout for structures with multiple models or
870 multiple sequences in alignment</li>
871 <li>Cannot import or associated local PDB files without a
872 PDB ID HEADER line</li>
873 <li>RMSD is not output in Jmol console when superposition
875 <li>Drag and drop of URL from Browser fails for Linux and
876 OSX versions earlier than El Capitan</li>
877 <li>ENA client ignores invalid content from ENA server</li>
878 <li>Exceptions are not raised in console when ENA client
879 attempts to fetch non-existent IDs via Fetch DB Refs UI
881 <li>Exceptions are not raised in console when a new view
882 is created on the alignment</li>
883 <li>OSX right-click fixed for group selections: CMD-click
884 to insert/remove gaps in groups and CTRL-click to open group
887 <em>Build and deployment</em>
889 <li>URL link checker now copes with multi-line anchor
892 <em>New Known Issues</em>
894 <li>Drag and drop from URL links in browsers do not work
901 <td width="60" nowrap>
903 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
909 <!-- JAL-2124 -->Updated Spanish translations.
912 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
913 for importing structure data to Jalview. Enables mmCIF and
917 <!-- JAL-192 --->Alignment ruler shows positions relative to
921 <!-- JAL-2202 -->Position/residue shown in status bar when
922 mousing over sequence associated annotation
925 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
929 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
930 '()', canonical '[]' and invalid '{}' base pair populations
934 <!-- JAL-2092 -->Feature settings popup menu options for
935 showing or hiding columns containing a feature
938 <!-- JAL-1557 -->Edit selected group by double clicking on
939 group and sequence associated annotation labels
942 <!-- JAL-2236 -->Sequence name added to annotation label in
943 select/hide columns by annotation and colour by annotation
947 </ul> <em>Application</em>
950 <!-- JAL-2050-->Automatically hide introns when opening a
954 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
958 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
959 structure mappings with the EMBL-EBI PDBe SIFTS database
962 <!-- JAL-2079 -->Updated download sites used for Rfam and
963 Pfam sources to xfam.org
966 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
969 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
970 over sequences in Jalview
973 <!-- JAL-2027-->Support for reverse-complement coding
974 regions in ENA and EMBL
977 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
978 for record retrieval via ENA rest API
981 <!-- JAL-2027 -->Support for ENA CDS records with reverse
985 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
986 groovy script execution
989 <!-- JAL-1812 -->New 'execute Groovy script' option in an
990 alignment window's Calculate menu
993 <!-- JAL-1812 -->Allow groovy scripts that call
994 Jalview.getAlignFrames() to run in headless mode
997 <!-- JAL-2068 -->Support for creating new alignment
998 calculation workers from groovy scripts
1001 <!-- JAL-1369 --->Store/restore reference sequence in
1005 <!-- JAL-1803 -->Chain codes for a sequence's PDB
1006 associations are now saved/restored from project
1009 <!-- JAL-1993 -->Database selection dialog always shown
1010 before sequence fetcher is opened
1013 <!-- JAL-2183 -->Double click on an entry in Jalview's
1014 database chooser opens a sequence fetcher
1017 <!-- JAL-1563 -->Free-text search client for UniProt using
1018 the UniProt REST API
1021 <!-- JAL-2168 -->-nonews command line parameter to prevent
1022 the news reader opening
1025 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
1026 querying stored in preferences
1029 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
1033 <!-- JAL-1977-->Tooltips shown on database chooser
1036 <!-- JAL-391 -->Reverse complement function in calculate
1037 menu for nucleotide sequences
1040 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
1041 and feature counts preserves alignment ordering (and
1042 debugged for complex feature sets).
1045 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1046 viewing structures with Jalview 2.10
1049 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1050 genome, transcript CCDS and gene ids via the Ensembl and
1051 Ensembl Genomes REST API
1054 <!-- JAL-2049 -->Protein sequence variant annotation
1055 computed for 'sequence_variant' annotation on CDS regions
1059 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1063 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1064 Ref Fetcher fails to match, or otherwise updates sequence
1065 data from external database records.
1068 <!-- JAL-2154 -->Revised Jalview Project format for
1069 efficient recovery of sequence coding and alignment
1070 annotation relationships.
1072 </ul> <!-- <em>Applet</em>
1083 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1087 <!-- JAL-2018-->Export features in Jalview format (again)
1088 includes graduated colourschemes
1091 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1092 working with big alignments and lots of hidden columns
1095 <!-- JAL-2053-->Hidden column markers not always rendered
1096 at right of alignment window
1099 <!-- JAL-2067 -->Tidied up links in help file table of
1103 <!-- JAL-2072 -->Feature based tree calculation not shown
1107 <!-- JAL-2075 -->Hidden columns ignored during feature
1108 based tree calculation
1111 <!-- JAL-2065 -->Alignment view stops updating when show
1112 unconserved enabled for group on alignment
1115 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1119 <!-- JAL-2146 -->Alignment column in status incorrectly
1120 shown as "Sequence position" when mousing over
1124 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1125 hidden columns present
1128 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1129 user created annotation added to alignment
1132 <!-- JAL-1841 -->RNA Structure consensus only computed for
1133 '()' base pair annotation
1136 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1137 in zero scores for all base pairs in RNA Structure
1141 <!-- JAL-2174-->Extend selection with columns containing
1145 <!-- JAL-2275 -->Pfam format writer puts extra space at
1146 beginning of sequence
1149 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1153 <!-- JAL-2238 -->Cannot create groups on an alignment from
1154 from a tree when t-coffee scores are shown
1157 <!-- JAL-1836,1967 -->Cannot import and view PDB
1158 structures with chains containing negative resnums (4q4h)
1161 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1165 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1166 to Clustal, PIR and PileUp output
1169 <!-- JAL-2008 -->Reordering sequence features that are
1170 not visible causes alignment window to repaint
1173 <!-- JAL-2006 -->Threshold sliders don't work in
1174 graduated colour and colour by annotation row for e-value
1175 scores associated with features and annotation rows
1178 <!-- JAL-1797 -->amino acid physicochemical conservation
1179 calculation should be case independent
1182 <!-- JAL-2173 -->Remove annotation also updates hidden
1186 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1187 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1188 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1191 <!-- JAL-2065 -->Null pointer exceptions and redraw
1192 problems when reference sequence defined and 'show
1193 non-conserved' enabled
1196 <!-- JAL-1306 -->Quality and Conservation are now shown on
1197 load even when Consensus calculation is disabled
1200 <!-- JAL-1932 -->Remove right on penultimate column of
1201 alignment does nothing
1204 <em>Application</em>
1207 <!-- JAL-1552-->URLs and links can't be imported by
1208 drag'n'drop on OSX when launched via webstart (note - not
1209 yet fixed for El Capitan)
1212 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1213 output when running on non-gb/us i18n platforms
1216 <!-- JAL-1944 -->Error thrown when exporting a view with
1217 hidden sequences as flat-file alignment
1220 <!-- JAL-2030-->InstallAnywhere distribution fails when
1224 <!-- JAL-2080-->Jalview very slow to launch via webstart
1225 (also hotfix for 2.9.0b2)
1228 <!-- JAL-2085 -->Cannot save project when view has a
1229 reference sequence defined
1232 <!-- JAL-1011 -->Columns are suddenly selected in other
1233 alignments and views when revealing hidden columns
1236 <!-- JAL-1989 -->Hide columns not mirrored in complement
1237 view in a cDNA/Protein splitframe
1240 <!-- JAL-1369 -->Cannot save/restore representative
1241 sequence from project when only one sequence is
1245 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1246 in Structure Chooser
1249 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1250 structure consensus didn't refresh annotation panel
1253 <!-- JAL-1962 -->View mapping in structure view shows
1254 mappings between sequence and all chains in a PDB file
1257 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1258 dialogs format columns correctly, don't display array
1259 data, sort columns according to type
1262 <!-- JAL-1975 -->Export complete shown after destination
1263 file chooser is cancelled during an image export
1266 <!-- JAL-2025 -->Error when querying PDB Service with
1267 sequence name containing special characters
1270 <!-- JAL-2024 -->Manual PDB structure querying should be
1274 <!-- JAL-2104 -->Large tooltips with broken HTML
1275 formatting don't wrap
1278 <!-- JAL-1128 -->Figures exported from wrapped view are
1279 truncated so L looks like I in consensus annotation
1282 <!-- JAL-2003 -->Export features should only export the
1283 currently displayed features for the current selection or
1287 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1288 after fetching cross-references, and restoring from
1292 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1293 followed in the structure viewer
1296 <!-- JAL-2163 -->Titles for individual alignments in
1297 splitframe not restored from project
1300 <!-- JAL-2145 -->missing autocalculated annotation at
1301 trailing end of protein alignment in transcript/product
1302 splitview when pad-gaps not enabled by default
1305 <!-- JAL-1797 -->amino acid physicochemical conservation
1309 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1310 article has been read (reopened issue due to
1311 internationalisation problems)
1314 <!-- JAL-1960 -->Only offer PDB structures in structure
1315 viewer based on sequence name, PDB and UniProt
1320 <!-- JAL-1976 -->No progress bar shown during export of
1324 <!-- JAL-2213 -->Structures not always superimposed after
1325 multiple structures are shown for one or more sequences.
1328 <!-- JAL-1370 -->Reference sequence characters should not
1329 be replaced with '.' when 'Show unconserved' format option
1333 <!-- JAL-1823 -->Cannot specify chain code when entering
1334 specific PDB id for sequence
1337 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1338 'Export hidden sequences' is enabled, but 'export hidden
1339 columns' is disabled.
1342 <!--JAL-2026-->Best Quality option in structure chooser
1343 selects lowest rather than highest resolution structures
1347 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1348 to sequence mapping in 'View Mappings' report
1351 <!-- JAL-2284 -->Unable to read old Jalview projects that
1352 contain non-XML data added after Jalvew wrote project.
1355 <!-- JAL-2118 -->Newly created annotation row reorders
1356 after clicking on it to create new annotation for a
1359 <!-- may exclude, this is an external service stability issue JAL-1941
1360 -- > RNA 3D structure not added via DSSR service</li> -->
1365 <!-- JAL-2151 -->Incorrect columns are selected when
1366 hidden columns present before start of sequence
1369 <!-- JAL-1986 -->Missing dependencies on applet pages
1373 <!-- JAL-1947 -->Overview pixel size changes when
1374 sequences are hidden in applet
1377 <!-- JAL-1996 -->Updated instructions for applet
1378 deployment on examples pages.
1385 <td width="60" nowrap>
1386 <div align="center">
1387 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1388 <em>16/10/2015</em></strong>
1391 <td><em>General</em>
1393 <li>Time stamps for signed Jalview application and applet
1398 <em>Application</em>
1400 <li>Duplicate group consensus and conservation rows
1401 shown when tree is partitioned</li>
1402 <li>Erratic behaviour when tree partitions made with
1403 multiple cDNA/Protein split views</li>
1409 <td width="60" nowrap>
1410 <div align="center">
1411 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1412 <em>8/10/2015</em></strong>
1415 <td><em>General</em>
1417 <li>Updated Spanish translations of localized text for
1419 </ul> <em>Application</em>
1421 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1422 <li>Signed OSX InstallAnywhere installer<br></li>
1423 <li>Support for per-sequence based annotations in BioJSON</li>
1424 </ul> <em>Applet</em>
1426 <li>Split frame example added to applet examples page</li>
1427 </ul> <em>Build and Deployment</em>
1430 <!-- JAL-1888 -->New ant target for running Jalview's test
1438 <li>Mapping of cDNA to protein in split frames
1439 incorrect when sequence start > 1</li>
1440 <li>Broken images in filter column by annotation dialog
1442 <li>Feature colours not parsed from features file</li>
1443 <li>Exceptions and incomplete link URLs recovered when
1444 loading a features file containing HTML tags in feature
1448 <em>Application</em>
1450 <li>Annotations corrupted after BioJS export and
1452 <li>Incorrect sequence limits after Fetch DB References
1453 with 'trim retrieved sequences'</li>
1454 <li>Incorrect warning about deleting all data when
1455 deleting selected columns</li>
1456 <li>Patch to build system for shipping properly signed
1457 JNLP templates for webstart launch</li>
1458 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1459 unreleased structures for download or viewing</li>
1460 <li>Tab/space/return keystroke operation of EMBL-PDBe
1461 fetcher/viewer dialogs works correctly</li>
1462 <li>Disabled 'minimise' button on Jalview windows
1463 running on OSX to workaround redraw hang bug</li>
1464 <li>Split cDNA/Protein view position and geometry not
1465 recovered from jalview project</li>
1466 <li>Initial enabled/disabled state of annotation menu
1467 sorter 'show autocalculated first/last' corresponds to
1469 <li>Restoring of Clustal, RNA Helices and T-Coffee
1470 color schemes from BioJSON</li>
1474 <li>Reorder sequences mirrored in cDNA/Protein split
1476 <li>Applet with Jmol examples not loading correctly</li>
1482 <td><div align="center">
1483 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1485 <td><em>General</em>
1487 <li>Linked visualisation and analysis of DNA and Protein
1490 <li>Translated cDNA alignments shown as split protein
1491 and DNA alignment views</li>
1492 <li>Codon consensus annotation for linked protein and
1493 cDNA alignment views</li>
1494 <li>Link cDNA or Protein product sequences by loading
1495 them onto Protein or cDNA alignments</li>
1496 <li>Reconstruct linked cDNA alignment from aligned
1497 protein sequences</li>
1500 <li>Jmol integration updated to Jmol v14.2.14</li>
1501 <li>Import and export of Jalview alignment views as <a
1502 href="features/bioJsonFormat.html">BioJSON</a></li>
1503 <li>New alignment annotation file statements for
1504 reference sequences and marking hidden columns</li>
1505 <li>Reference sequence based alignment shading to
1506 highlight variation</li>
1507 <li>Select or hide columns according to alignment
1509 <li>Find option for locating sequences by description</li>
1510 <li>Conserved physicochemical properties shown in amino
1511 acid conservation row</li>
1512 <li>Alignments can be sorted by number of RNA helices</li>
1513 </ul> <em>Application</em>
1515 <li>New cDNA/Protein analysis capabilities
1517 <li>Get Cross-References should open a Split Frame
1518 view with cDNA/Protein</li>
1519 <li>Detect when nucleotide sequences and protein
1520 sequences are placed in the same alignment</li>
1521 <li>Split cDNA/Protein views are saved in Jalview
1526 <li>Use REST API to talk to Chimera</li>
1527 <li>Selected regions in Chimera are highlighted in linked
1528 Jalview windows</li>
1530 <li>VARNA RNA viewer updated to v3.93</li>
1531 <li>VARNA views are saved in Jalview Projects</li>
1532 <li>Pseudoknots displayed as Jalview RNA annotation can
1533 be shown in VARNA</li>
1535 <li>Make groups for selection uses marked columns as well
1536 as the active selected region</li>
1538 <li>Calculate UPGMA and NJ trees using sequence feature
1540 <li>New Export options
1542 <li>New Export Settings dialog to control hidden
1543 region export in flat file generation</li>
1545 <li>Export alignment views for display with the <a
1546 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1548 <li>Export scrollable SVG in HTML page</li>
1549 <li>Optional embedding of BioJSON data when exporting
1550 alignment figures to HTML</li>
1552 <li>3D structure retrieval and display
1554 <li>Free text and structured queries with the PDBe
1556 <li>PDBe Search API based discovery and selection of
1557 PDB structures for a sequence set</li>
1561 <li>JPred4 employed for protein secondary structure
1563 <li>Hide Insertions menu option to hide unaligned columns
1564 for one or a group of sequences</li>
1565 <li>Automatically hide insertions in alignments imported
1566 from the JPred4 web server</li>
1567 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1568 system on OSX<br />LGPL libraries courtesy of <a
1569 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1571 <li>changed 'View nucleotide structure' submenu to 'View
1572 VARNA 2D Structure'</li>
1573 <li>change "View protein structure" menu option to "3D
1576 </ul> <em>Applet</em>
1578 <li>New layout for applet example pages</li>
1579 <li>New parameters to enable SplitFrame view
1580 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1581 <li>New example demonstrating linked viewing of cDNA and
1582 Protein alignments</li>
1583 </ul> <em>Development and deployment</em>
1585 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1586 <li>Include installation type and git revision in build
1587 properties and console log output</li>
1588 <li>Jalview Github organisation, and new github site for
1589 storing BioJsMSA Templates</li>
1590 <li>Jalview's unit tests now managed with TestNG</li>
1593 <!-- <em>General</em>
1595 </ul> --> <!-- issues resolved --> <em>Application</em>
1597 <li>Escape should close any open find dialogs</li>
1598 <li>Typo in select-by-features status report</li>
1599 <li>Consensus RNA secondary secondary structure
1600 predictions are not highlighted in amber</li>
1601 <li>Missing gap character in v2.7 example file means
1602 alignment appears unaligned when pad-gaps is not enabled</li>
1603 <li>First switch to RNA Helices colouring doesn't colour
1604 associated structure views</li>
1605 <li>ID width preference option is greyed out when auto
1606 width checkbox not enabled</li>
1607 <li>Stopped a warning dialog from being shown when
1608 creating user defined colours</li>
1609 <li>'View Mapping' in structure viewer shows sequence
1610 mappings for just that viewer's sequences</li>
1611 <li>Workaround for superposing PDB files containing
1612 multiple models in Chimera</li>
1613 <li>Report sequence position in status bar when hovering
1614 over Jmol structure</li>
1615 <li>Cannot output gaps as '.' symbols with Selection ->
1616 output to text box</li>
1617 <li>Flat file exports of alignments with hidden columns
1618 have incorrect sequence start/end</li>
1619 <li>'Aligning' a second chain to a Chimera structure from
1621 <li>Colour schemes applied to structure viewers don't
1622 work for nucleotide</li>
1623 <li>Loading/cut'n'pasting an empty or invalid file leads
1624 to a grey/invisible alignment window</li>
1625 <li>Exported Jpred annotation from a sequence region
1626 imports to different position</li>
1627 <li>Space at beginning of sequence feature tooltips shown
1628 on some platforms</li>
1629 <li>Chimera viewer 'View | Show Chain' menu is not
1631 <li>'New View' fails with a Null Pointer Exception in
1632 console if Chimera has been opened</li>
1633 <li>Mouseover to Chimera not working</li>
1634 <li>Miscellaneous ENA XML feature qualifiers not
1636 <li>NPE in annotation renderer after 'Extract Scores'</li>
1637 <li>If two structures in one Chimera window, mouseover of
1638 either sequence shows on first structure</li>
1639 <li>'Show annotations' options should not make
1640 non-positional annotations visible</li>
1641 <li>Subsequence secondary structure annotation not shown
1642 in right place after 'view flanking regions'</li>
1643 <li>File Save As type unset when current file format is
1645 <li>Save as '.jar' option removed for saving Jalview
1647 <li>Colour by Sequence colouring in Chimera more
1649 <li>Cannot 'add reference annotation' for a sequence in
1650 several views on same alignment</li>
1651 <li>Cannot show linked products for EMBL / ENA records</li>
1652 <li>Jalview's tooltip wraps long texts containing no
1654 </ul> <em>Applet</em>
1656 <li>Jmol to JalviewLite mouseover/link not working</li>
1657 <li>JalviewLite can't import sequences with ID
1658 descriptions containing angle brackets</li>
1659 </ul> <em>General</em>
1661 <li>Cannot export and reimport RNA secondary structure
1662 via jalview annotation file</li>
1663 <li>Random helix colour palette for colour by annotation
1664 with RNA secondary structure</li>
1665 <li>Mouseover to cDNA from STOP residue in protein
1666 translation doesn't work.</li>
1667 <li>hints when using the select by annotation dialog box</li>
1668 <li>Jmol alignment incorrect if PDB file has alternate CA
1670 <li>FontChooser message dialog appears to hang after
1671 choosing 1pt font</li>
1672 <li>Peptide secondary structure incorrectly imported from
1673 annotation file when annotation display text includes 'e' or
1675 <li>Cannot set colour of new feature type whilst creating
1677 <li>cDNA translation alignment should not be sequence
1678 order dependent</li>
1679 <li>'Show unconserved' doesn't work for lower case
1681 <li>Nucleotide ambiguity codes involving R not recognised</li>
1682 </ul> <em>Deployment and Documentation</em>
1684 <li>Applet example pages appear different to the rest of
1685 www.jalview.org</li>
1686 </ul> <em>Application Known issues</em>
1688 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1689 <li>Misleading message appears after trying to delete
1691 <li>Jalview icon not shown in dock after InstallAnywhere
1692 version launches</li>
1693 <li>Fetching EMBL reference for an RNA sequence results
1694 fails with a sequence mismatch</li>
1695 <li>Corrupted or unreadable alignment display when
1696 scrolling alignment to right</li>
1697 <li>ArrayIndexOutOfBoundsException thrown when remove
1698 empty columns called on alignment with ragged gapped ends</li>
1699 <li>auto calculated alignment annotation rows do not get
1700 placed above or below non-autocalculated rows</li>
1701 <li>Jalview dekstop becomes sluggish at full screen in
1702 ultra-high resolution</li>
1703 <li>Cannot disable consensus calculation independently of
1704 quality and conservation</li>
1705 <li>Mouseover highlighting between cDNA and protein can
1706 become sluggish with more than one splitframe shown</li>
1707 </ul> <em>Applet Known Issues</em>
1709 <li>Core PDB parsing code requires Jmol</li>
1710 <li>Sequence canvas panel goes white when alignment
1711 window is being resized</li>
1717 <td><div align="center">
1718 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1720 <td><em>General</em>
1722 <li>Updated Java code signing certificate donated by
1724 <li>Features and annotation preserved when performing
1725 pairwise alignment</li>
1726 <li>RNA pseudoknot annotation can be
1727 imported/exported/displayed</li>
1728 <li>'colour by annotation' can colour by RNA and
1729 protein secondary structure</li>
1730 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1731 post-hoc with 2.9 release</em>)
1734 </ul> <em>Application</em>
1736 <li>Extract and display secondary structure for sequences
1737 with 3D structures</li>
1738 <li>Support for parsing RNAML</li>
1739 <li>Annotations menu for layout
1741 <li>sort sequence annotation rows by alignment</li>
1742 <li>place sequence annotation above/below alignment
1745 <li>Output in Stockholm format</li>
1746 <li>Internationalisation: improved Spanish (es)
1748 <li>Structure viewer preferences tab</li>
1749 <li>Disorder and Secondary Structure annotation tracks
1750 shared between alignments</li>
1751 <li>UCSF Chimera launch and linked highlighting from
1753 <li>Show/hide all sequence associated annotation rows for
1754 all or current selection</li>
1755 <li>disorder and secondary structure predictions
1756 available as dataset annotation</li>
1757 <li>Per-sequence rna helices colouring</li>
1760 <li>Sequence database accessions imported when fetching
1761 alignments from Rfam</li>
1762 <li>update VARNA version to 3.91</li>
1764 <li>New groovy scripts for exporting aligned positions,
1765 conservation values, and calculating sum of pairs scores.</li>
1766 <li>Command line argument to set default JABAWS server</li>
1767 <li>include installation type in build properties and
1768 console log output</li>
1769 <li>Updated Jalview project format to preserve dataset
1773 <!-- issues resolved --> <em>Application</em>
1775 <li>Distinguish alignment and sequence associated RNA
1776 structure in structure->view->VARNA</li>
1777 <li>Raise dialog box if user deletes all sequences in an
1779 <li>Pressing F1 results in documentation opening twice</li>
1780 <li>Sequence feature tooltip is wrapped</li>
1781 <li>Double click on sequence associated annotation
1782 selects only first column</li>
1783 <li>Redundancy removal doesn't result in unlinked
1784 leaves shown in tree</li>
1785 <li>Undos after several redundancy removals don't undo
1787 <li>Hide sequence doesn't hide associated annotation</li>
1788 <li>User defined colours dialog box too big to fit on
1789 screen and buttons not visible</li>
1790 <li>author list isn't updated if already written to
1791 Jalview properties</li>
1792 <li>Popup menu won't open after retrieving sequence
1794 <li>File open window for associate PDB doesn't open</li>
1795 <li>Left-then-right click on a sequence id opens a
1796 browser search window</li>
1797 <li>Cannot open sequence feature shading/sort popup menu
1798 in feature settings dialog</li>
1799 <li>better tooltip placement for some areas of Jalview
1801 <li>Allow addition of JABAWS Server which doesn't
1802 pass validation</li>
1803 <li>Web services parameters dialog box is too large to
1805 <li>Muscle nucleotide alignment preset obscured by
1807 <li>JABAWS preset submenus don't contain newly
1808 defined user preset</li>
1809 <li>MSA web services warns user if they were launched
1810 with invalid input</li>
1811 <li>Jalview cannot contact DAS Registy when running on
1814 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1815 'Superpose with' submenu not shown when new view
1819 </ul> <!-- <em>Applet</em>
1821 </ul> <em>General</em>
1823 </ul>--> <em>Deployment and Documentation</em>
1825 <li>2G and 1G options in launchApp have no effect on
1826 memory allocation</li>
1827 <li>launchApp service doesn't automatically open
1828 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1830 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1831 InstallAnywhere reports cannot find valid JVM when Java
1832 1.7_055 is available
1834 </ul> <em>Application Known issues</em>
1837 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1838 corrupted or unreadable alignment display when scrolling
1842 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1843 retrieval fails but progress bar continues for DAS retrieval
1844 with large number of ID
1847 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1848 flatfile output of visible region has incorrect sequence
1852 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1853 rna structure consensus doesn't update when secondary
1854 structure tracks are rearranged
1857 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1858 invalid rna structure positional highlighting does not
1859 highlight position of invalid base pairs
1862 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1863 out of memory errors are not raised when saving Jalview
1864 project from alignment window file menu
1867 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1868 Switching to RNA Helices colouring doesn't propagate to
1872 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1873 colour by RNA Helices not enabled when user created
1874 annotation added to alignment
1877 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1878 Jalview icon not shown on dock in Mountain Lion/Webstart
1880 </ul> <em>Applet Known Issues</em>
1883 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1884 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1887 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1888 Jalview and Jmol example not compatible with IE9
1891 <li>Sort by annotation score doesn't reverse order
1897 <td><div align="center">
1898 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1901 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1904 <li>Internationalisation of user interface (usually
1905 called i18n support) and translation for Spanish locale</li>
1906 <li>Define/Undefine group on current selection with
1907 Ctrl-G/Shift Ctrl-G</li>
1908 <li>Improved group creation/removal options in
1909 alignment/sequence Popup menu</li>
1910 <li>Sensible precision for symbol distribution
1911 percentages shown in logo tooltip.</li>
1912 <li>Annotation panel height set according to amount of
1913 annotation when alignment first opened</li>
1914 </ul> <em>Application</em>
1916 <li>Interactive consensus RNA secondary structure
1917 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1918 <li>Select columns containing particular features from
1919 Feature Settings dialog</li>
1920 <li>View all 'representative' PDB structures for selected
1922 <li>Update Jalview project format:
1924 <li>New file extension for Jalview projects '.jvp'</li>
1925 <li>Preserve sequence and annotation dataset (to
1926 store secondary structure annotation,etc)</li>
1927 <li>Per group and alignment annotation and RNA helix
1931 <li>New similarity measures for PCA and Tree calculation
1933 <li>Experimental support for retrieval and viewing of
1934 flanking regions for an alignment</li>
1938 <!-- issues resolved --> <em>Application</em>
1940 <li>logo keeps spinning and status remains at queued or
1941 running after job is cancelled</li>
1942 <li>cannot export features from alignments imported from
1943 Jalview/VAMSAS projects</li>
1944 <li>Buggy slider for web service parameters that take
1946 <li>Newly created RNA secondary structure line doesn't
1947 have 'display all symbols' flag set</li>
1948 <li>T-COFFEE alignment score shading scheme and other
1949 annotation shading not saved in Jalview project</li>
1950 <li>Local file cannot be loaded in freshly downloaded
1952 <li>Jalview icon not shown on dock in Mountain
1954 <li>Load file from desktop file browser fails</li>
1955 <li>Occasional NPE thrown when calculating large trees</li>
1956 <li>Cannot reorder or slide sequences after dragging an
1957 alignment onto desktop</li>
1958 <li>Colour by annotation dialog throws NPE after using
1959 'extract scores' function</li>
1960 <li>Loading/cut'n'pasting an empty file leads to a grey
1961 alignment window</li>
1962 <li>Disorder thresholds rendered incorrectly after
1963 performing IUPred disorder prediction</li>
1964 <li>Multiple group annotated consensus rows shown when
1965 changing 'normalise logo' display setting</li>
1966 <li>Find shows blank dialog after 'finished searching' if
1967 nothing matches query</li>
1968 <li>Null Pointer Exceptions raised when sorting by
1969 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1971 <li>Errors in Jmol console when structures in alignment
1972 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1974 <li>Not all working JABAWS services are shown in
1976 <li>JAVAWS version of Jalview fails to launch with
1977 'invalid literal/length code'</li>
1978 <li>Annotation/RNA Helix colourschemes cannot be applied
1979 to alignment with groups (actually fixed in 2.8.0b1)</li>
1980 <li>RNA Helices and T-Coffee Scores available as default
1983 </ul> <em>Applet</em>
1985 <li>Remove group option is shown even when selection is
1987 <li>Apply to all groups ticked but colourscheme changes
1988 don't affect groups</li>
1989 <li>Documented RNA Helices and T-Coffee Scores as valid
1990 colourscheme name</li>
1991 <li>Annotation labels drawn on sequence IDs when
1992 Annotation panel is not displayed</li>
1993 <li>Increased font size for dropdown menus on OSX and
1994 embedded windows</li>
1995 </ul> <em>Other</em>
1997 <li>Consensus sequence for alignments/groups with a
1998 single sequence were not calculated</li>
1999 <li>annotation files that contain only groups imported as
2000 annotation and junk sequences</li>
2001 <li>Fasta files with sequences containing '*' incorrectly
2002 recognised as PFAM or BLC</li>
2003 <li>conservation/PID slider apply all groups option
2004 doesn't affect background (2.8.0b1)
2006 <li>redundancy highlighting is erratic at 0% and 100%</li>
2007 <li>Remove gapped columns fails for sequences with ragged
2009 <li>AMSA annotation row with leading spaces is not
2010 registered correctly on import</li>
2011 <li>Jalview crashes when selecting PCA analysis for
2012 certain alignments</li>
2013 <li>Opening the colour by annotation dialog for an
2014 existing annotation based 'use original colours'
2015 colourscheme loses original colours setting</li>
2020 <td><div align="center">
2021 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
2022 <em>30/1/2014</em></strong>
2026 <li>Trusted certificates for JalviewLite applet and
2027 Jalview Desktop application<br />Certificate was donated by
2028 <a href="https://www.certum.eu">Certum</a> to the Jalview
2029 open source project).
2031 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
2032 <li>Output in Stockholm format</li>
2033 <li>Allow import of data from gzipped files</li>
2034 <li>Export/import group and sequence associated line
2035 graph thresholds</li>
2036 <li>Nucleotide substitution matrix that supports RNA and
2037 ambiguity codes</li>
2038 <li>Allow disorder predictions to be made on the current
2039 selection (or visible selection) in the same way that JPred
2041 <li>Groovy scripting for headless Jalview operation</li>
2042 </ul> <em>Other improvements</em>
2044 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
2045 <li>COMBINE statement uses current SEQUENCE_REF and
2046 GROUP_REF scope to group annotation rows</li>
2047 <li>Support '' style escaping of quotes in Newick
2049 <li>Group options for JABAWS service by command line name</li>
2050 <li>Empty tooltip shown for JABA service options with a
2051 link but no description</li>
2052 <li>Select primary source when selecting authority in
2053 database fetcher GUI</li>
2054 <li>Add .mfa to FASTA file extensions recognised by
2056 <li>Annotation label tooltip text wrap</li>
2061 <li>Slow scrolling when lots of annotation rows are
2063 <li>Lots of NPE (and slowness) after creating RNA
2064 secondary structure annotation line</li>
2065 <li>Sequence database accessions not imported when
2066 fetching alignments from Rfam</li>
2067 <li>Incorrect SHMR submission for sequences with
2069 <li>View all structures does not always superpose
2071 <li>Option widgets in service parameters not updated to
2072 reflect user or preset settings</li>
2073 <li>Null pointer exceptions for some services without
2074 presets or adjustable parameters</li>
2075 <li>Discover PDB IDs entry in structure menu doesn't
2076 discover PDB xRefs</li>
2077 <li>Exception encountered while trying to retrieve
2078 features with DAS</li>
2079 <li>Lowest value in annotation row isn't coloured
2080 when colour by annotation (per sequence) is coloured</li>
2081 <li>Keyboard mode P jumps to start of gapped region when
2082 residue follows a gap</li>
2083 <li>Jalview appears to hang importing an alignment with
2084 Wrap as default or after enabling Wrap</li>
2085 <li>'Right click to add annotations' message
2086 shown in wrap mode when no annotations present</li>
2087 <li>Disorder predictions fail with NPE if no automatic
2088 annotation already exists on alignment</li>
2089 <li>oninit javascript function should be called after
2090 initialisation completes</li>
2091 <li>Remove redundancy after disorder prediction corrupts
2092 alignment window display</li>
2093 <li>Example annotation file in documentation is invalid</li>
2094 <li>Grouped line graph annotation rows are not exported
2095 to annotation file</li>
2096 <li>Multi-harmony analysis cannot be run when only two
2098 <li>Cannot create multiple groups of line graphs with
2099 several 'combine' statements in annotation file</li>
2100 <li>Pressing return several times causes Number Format
2101 exceptions in keyboard mode</li>
2102 <li>Multi-harmony (SHMMR) method doesn't submit
2103 correct partitions for input data</li>
2104 <li>Translation from DNA to Amino Acids fails</li>
2105 <li>Jalview fail to load newick tree with quoted label</li>
2106 <li>--headless flag isn't understood</li>
2107 <li>ClassCastException when generating EPS in headless
2109 <li>Adjusting sequence-associated shading threshold only
2110 changes one row's threshold</li>
2111 <li>Preferences and Feature settings panel panel
2112 doesn't open</li>
2113 <li>hide consensus histogram also hides conservation and
2114 quality histograms</li>
2119 <td><div align="center">
2120 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2122 <td><em>Application</em>
2124 <li>Support for JABAWS 2.0 Services (AACon alignment
2125 conservation, protein disorder and Clustal Omega)</li>
2126 <li>JABAWS server status indicator in Web Services
2128 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2129 in Jalview alignment window</li>
2130 <li>Updated Jalview build and deploy framework for OSX
2131 mountain lion, windows 7, and 8</li>
2132 <li>Nucleotide substitution matrix for PCA that supports
2133 RNA and ambiguity codes</li>
2135 <li>Improved sequence database retrieval GUI</li>
2136 <li>Support fetching and database reference look up
2137 against multiple DAS sources (Fetch all from in 'fetch db
2139 <li>Jalview project improvements
2141 <li>Store and retrieve the 'belowAlignment'
2142 flag for annotation</li>
2143 <li>calcId attribute to group annotation rows on the
2145 <li>Store AACon calculation settings for a view in
2146 Jalview project</li>
2150 <li>horizontal scrolling gesture support</li>
2151 <li>Visual progress indicator when PCA calculation is
2153 <li>Simpler JABA web services menus</li>
2154 <li>visual indication that web service results are still
2155 being retrieved from server</li>
2156 <li>Serialise the dialogs that are shown when Jalview
2157 starts up for first time</li>
2158 <li>Jalview user agent string for interacting with HTTP
2160 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2162 <li>Examples directory and Groovy library included in
2163 InstallAnywhere distribution</li>
2164 </ul> <em>Applet</em>
2166 <li>RNA alignment and secondary structure annotation
2167 visualization applet example</li>
2168 </ul> <em>General</em>
2170 <li>Normalise option for consensus sequence logo</li>
2171 <li>Reset button in PCA window to return dimensions to
2173 <li>Allow seqspace or Jalview variant of alignment PCA
2175 <li>PCA with either nucleic acid and protein substitution
2177 <li>Allow windows containing HTML reports to be exported
2179 <li>Interactive display and editing of RNA secondary
2180 structure contacts</li>
2181 <li>RNA Helix Alignment Colouring</li>
2182 <li>RNA base pair logo consensus</li>
2183 <li>Parse sequence associated secondary structure
2184 information in Stockholm files</li>
2185 <li>HTML Export database accessions and annotation
2186 information presented in tooltip for sequences</li>
2187 <li>Import secondary structure from LOCARNA clustalw
2188 style RNA alignment files</li>
2189 <li>import and visualise T-COFFEE quality scores for an
2191 <li>'colour by annotation' per sequence option to
2192 shade each sequence according to its associated alignment
2194 <li>New Jalview Logo</li>
2195 </ul> <em>Documentation and Development</em>
2197 <li>documentation for score matrices used in Jalview</li>
2198 <li>New Website!</li>
2200 <td><em>Application</em>
2202 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2203 wsdbfetch REST service</li>
2204 <li>Stop windows being moved outside desktop on OSX</li>
2205 <li>Filetype associations not installed for webstart
2207 <li>Jalview does not always retrieve progress of a JABAWS
2208 job execution in full once it is complete</li>
2209 <li>revise SHMR RSBS definition to ensure alignment is
2210 uploaded via ali_file parameter</li>
2211 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2212 <li>View all structures superposed fails with exception</li>
2213 <li>Jnet job queues forever if a very short sequence is
2214 submitted for prediction</li>
2215 <li>Cut and paste menu not opened when mouse clicked on
2217 <li>Putting fractional value into integer text box in
2218 alignment parameter dialog causes Jalview to hang</li>
2219 <li>Structure view highlighting doesn't work on
2221 <li>View all structures fails with exception shown in
2223 <li>Characters in filename associated with PDBEntry not
2224 escaped in a platform independent way</li>
2225 <li>Jalview desktop fails to launch with exception when
2227 <li>Tree calculation reports 'you must have 2 or more
2228 sequences selected' when selection is empty</li>
2229 <li>Jalview desktop fails to launch with jar signature
2230 failure when java web start temporary file caching is
2232 <li>DAS Sequence retrieval with range qualification
2233 results in sequence xref which includes range qualification</li>
2234 <li>Errors during processing of command line arguments
2235 cause progress bar (JAL-898) to be removed</li>
2236 <li>Replace comma for semi-colon option not disabled for
2237 DAS sources in sequence fetcher</li>
2238 <li>Cannot close news reader when JABAWS server warning
2239 dialog is shown</li>
2240 <li>Option widgets not updated to reflect user settings</li>
2241 <li>Edited sequence not submitted to web service</li>
2242 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2243 <li>InstallAnywhere installer doesn't unpack and run
2244 on OSX Mountain Lion</li>
2245 <li>Annotation panel not given a scroll bar when
2246 sequences with alignment annotation are pasted into the
2248 <li>Sequence associated annotation rows not associated
2249 when loaded from Jalview project</li>
2250 <li>Browser launch fails with NPE on java 1.7</li>
2251 <li>JABAWS alignment marked as finished when job was
2252 cancelled or job failed due to invalid input</li>
2253 <li>NPE with v2.7 example when clicking on Tree
2254 associated with all views</li>
2255 <li>Exceptions when copy/paste sequences with grouped
2256 annotation rows to new window</li>
2257 </ul> <em>Applet</em>
2259 <li>Sequence features are momentarily displayed before
2260 they are hidden using hidefeaturegroups applet parameter</li>
2261 <li>loading features via javascript API automatically
2262 enables feature display</li>
2263 <li>scrollToColumnIn javascript API method doesn't
2265 </ul> <em>General</em>
2267 <li>Redundancy removal fails for rna alignment</li>
2268 <li>PCA calculation fails when sequence has been selected
2269 and then deselected</li>
2270 <li>PCA window shows grey box when first opened on OSX</li>
2271 <li>Letters coloured pink in sequence logo when alignment
2272 coloured with clustalx</li>
2273 <li>Choosing fonts without letter symbols defined causes
2274 exceptions and redraw errors</li>
2275 <li>Initial PCA plot view is not same as manually
2276 reconfigured view</li>
2277 <li>Grouped annotation graph label has incorrect line
2279 <li>Grouped annotation graph label display is corrupted
2280 for lots of labels</li>
2285 <div align="center">
2286 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2289 <td><em>Application</em>
2291 <li>Jalview Desktop News Reader</li>
2292 <li>Tweaked default layout of web services menu</li>
2293 <li>View/alignment association menu to enable user to
2294 easily specify which alignment a multi-structure view takes
2295 its colours/correspondences from</li>
2296 <li>Allow properties file location to be specified as URL</li>
2297 <li>Extend Jalview project to preserve associations
2298 between many alignment views and a single Jmol display</li>
2299 <li>Store annotation row height in Jalview project file</li>
2300 <li>Annotation row column label formatting attributes
2301 stored in project file</li>
2302 <li>Annotation row order for auto-calculated annotation
2303 rows preserved in Jalview project file</li>
2304 <li>Visual progress indication when Jalview state is
2305 saved using Desktop window menu</li>
2306 <li>Visual indication that command line arguments are
2307 still being processed</li>
2308 <li>Groovy script execution from URL</li>
2309 <li>Colour by annotation default min and max colours in
2311 <li>Automatically associate PDB files dragged onto an
2312 alignment with sequences that have high similarity and
2314 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2315 <li>'view structures' option to open many
2316 structures in same window</li>
2317 <li>Sort associated views menu option for tree panel</li>
2318 <li>Group all JABA and non-JABA services for a particular
2319 analysis function in its own submenu</li>
2320 </ul> <em>Applet</em>
2322 <li>Userdefined and autogenerated annotation rows for
2324 <li>Adjustment of alignment annotation pane height</li>
2325 <li>Annotation scrollbar for annotation panel</li>
2326 <li>Drag to reorder annotation rows in annotation panel</li>
2327 <li>'automaticScrolling' parameter</li>
2328 <li>Allow sequences with partial ID string matches to be
2329 annotated from GFF/Jalview features files</li>
2330 <li>Sequence logo annotation row in applet</li>
2331 <li>Absolute paths relative to host server in applet
2332 parameters are treated as such</li>
2333 <li>New in the JalviewLite javascript API:
2335 <li>JalviewLite.js javascript library</li>
2336 <li>Javascript callbacks for
2338 <li>Applet initialisation</li>
2339 <li>Sequence/alignment mouse-overs and selections</li>
2342 <li>scrollTo row and column alignment scrolling
2344 <li>Select sequence/alignment regions from javascript</li>
2345 <li>javascript structure viewer harness to pass
2346 messages between Jmol and Jalview when running as
2347 distinct applets</li>
2348 <li>sortBy method</li>
2349 <li>Set of applet and application examples shipped
2350 with documentation</li>
2351 <li>New example to demonstrate JalviewLite and Jmol
2352 javascript message exchange</li>
2354 </ul> <em>General</em>
2356 <li>Enable Jmol displays to be associated with multiple
2357 multiple alignments</li>
2358 <li>Option to automatically sort alignment with new tree</li>
2359 <li>User configurable link to enable redirects to a
2360 www.Jalview.org mirror</li>
2361 <li>Jmol colours option for Jmol displays</li>
2362 <li>Configurable newline string when writing alignment
2363 and other flat files</li>
2364 <li>Allow alignment annotation description lines to
2365 contain html tags</li>
2366 </ul> <em>Documentation and Development</em>
2368 <li>Add groovy test harness for bulk load testing to
2370 <li>Groovy script to load and align a set of sequences
2371 using a web service before displaying the result in the
2372 Jalview desktop</li>
2373 <li>Restructured javascript and applet api documentation</li>
2374 <li>Ant target to publish example html files with applet
2376 <li>Netbeans project for building Jalview from source</li>
2377 <li>ant task to create online javadoc for Jalview source</li>
2379 <td><em>Application</em>
2381 <li>User defined colourscheme throws exception when
2382 current built in colourscheme is saved as new scheme</li>
2383 <li>AlignFrame->Save in application pops up save
2384 dialog for valid filename/format</li>
2385 <li>Cannot view associated structure for UniProt sequence</li>
2386 <li>PDB file association breaks for UniProt sequence
2388 <li>Associate PDB from file dialog does not tell you
2389 which sequence is to be associated with the file</li>
2390 <li>Find All raises null pointer exception when query
2391 only matches sequence IDs</li>
2392 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2393 <li>Jalview project with Jmol views created with Jalview
2394 2.4 cannot be loaded</li>
2395 <li>Filetype associations not installed for webstart
2397 <li>Two or more chains in a single PDB file associated
2398 with sequences in different alignments do not get coloured
2399 by their associated sequence</li>
2400 <li>Visibility status of autocalculated annotation row
2401 not preserved when project is loaded</li>
2402 <li>Annotation row height and visibility attributes not
2403 stored in Jalview project</li>
2404 <li>Tree bootstraps are not preserved when saved as a
2405 Jalview project</li>
2406 <li>Envision2 workflow tooltips are corrupted</li>
2407 <li>Enabling show group conservation also enables colour
2408 by conservation</li>
2409 <li>Duplicate group associated conservation or consensus
2410 created on new view</li>
2411 <li>Annotation scrollbar not displayed after 'show
2412 all hidden annotation rows' option selected</li>
2413 <li>Alignment quality not updated after alignment
2414 annotation row is hidden then shown</li>
2415 <li>Preserve colouring of structures coloured by
2416 sequences in pre Jalview 2.7 projects</li>
2417 <li>Web service job parameter dialog is not laid out
2419 <li>Web services menu not refreshed after 'reset
2420 services' button is pressed in preferences</li>
2421 <li>Annotation off by one in Jalview v2_3 example project</li>
2422 <li>Structures imported from file and saved in project
2423 get name like jalview_pdb1234.txt when reloaded</li>
2424 <li>Jalview does not always retrieve progress of a JABAWS
2425 job execution in full once it is complete</li>
2426 </ul> <em>Applet</em>
2428 <li>Alignment height set incorrectly when lots of
2429 annotation rows are displayed</li>
2430 <li>Relative URLs in feature HTML text not resolved to
2432 <li>View follows highlighting does not work for positions
2434 <li><= shown as = in tooltip</li>
2435 <li>Export features raises exception when no features
2437 <li>Separator string used for serialising lists of IDs
2438 for javascript api is modified when separator string
2439 provided as parameter</li>
2440 <li>Null pointer exception when selecting tree leaves for
2441 alignment with no existing selection</li>
2442 <li>Relative URLs for datasources assumed to be relative
2443 to applet's codebase</li>
2444 <li>Status bar not updated after finished searching and
2445 search wraps around to first result</li>
2446 <li>StructureSelectionManager instance shared between
2447 several Jalview applets causes race conditions and memory
2449 <li>Hover tooltip and mouseover of position on structure
2450 not sent from Jmol in applet</li>
2451 <li>Certain sequences of javascript method calls to
2452 applet API fatally hang browser</li>
2453 </ul> <em>General</em>
2455 <li>View follows structure mouseover scrolls beyond
2456 position with wrapped view and hidden regions</li>
2457 <li>Find sequence position moves to wrong residue
2458 with/without hidden columns</li>
2459 <li>Sequence length given in alignment properties window
2461 <li>InvalidNumberFormat exceptions thrown when trying to
2462 import PDB like structure files</li>
2463 <li>Positional search results are only highlighted
2464 between user-supplied sequence start/end bounds</li>
2465 <li>End attribute of sequence is not validated</li>
2466 <li>Find dialog only finds first sequence containing a
2467 given sequence position</li>
2468 <li>Sequence numbering not preserved in MSF alignment
2470 <li>Jalview PDB file reader does not extract sequence
2471 from nucleotide chains correctly</li>
2472 <li>Structure colours not updated when tree partition
2473 changed in alignment</li>
2474 <li>Sequence associated secondary structure not correctly
2475 parsed in interleaved stockholm</li>
2476 <li>Colour by annotation dialog does not restore current
2478 <li>Hiding (nearly) all sequences doesn't work
2480 <li>Sequences containing lowercase letters are not
2481 properly associated with their pdb files</li>
2482 </ul> <em>Documentation and Development</em>
2484 <li>schemas/JalviewWsParamSet.xsd corrupted by
2485 ApplyCopyright tool</li>
2490 <div align="center">
2491 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2494 <td><em>Application</em>
2496 <li>New warning dialog when the Jalview Desktop cannot
2497 contact web services</li>
2498 <li>JABA service parameters for a preset are shown in
2499 service job window</li>
2500 <li>JABA Service menu entries reworded</li>
2504 <li>Modeller PIR IO broken - cannot correctly import a
2505 pir file emitted by Jalview</li>
2506 <li>Existing feature settings transferred to new
2507 alignment view created from cut'n'paste</li>
2508 <li>Improved test for mixed amino/nucleotide chains when
2509 parsing PDB files</li>
2510 <li>Consensus and conservation annotation rows
2511 occasionally become blank for all new windows</li>
2512 <li>Exception raised when right clicking above sequences
2513 in wrapped view mode</li>
2514 </ul> <em>Application</em>
2516 <li>multiple multiply aligned structure views cause cpu
2517 usage to hit 100% and computer to hang</li>
2518 <li>Web Service parameter layout breaks for long user
2519 parameter names</li>
2520 <li>Jaba service discovery hangs desktop if Jaba server
2527 <div align="center">
2528 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2531 <td><em>Application</em>
2533 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2534 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2537 <li>Web Services preference tab</li>
2538 <li>Analysis parameters dialog box and user defined
2540 <li>Improved speed and layout of Envision2 service menu</li>
2541 <li>Superpose structures using associated sequence
2543 <li>Export coordinates and projection as CSV from PCA
2545 </ul> <em>Applet</em>
2547 <li>enable javascript: execution by the applet via the
2548 link out mechanism</li>
2549 </ul> <em>Other</em>
2551 <li>Updated the Jmol Jalview interface to work with Jmol
2553 <li>The Jalview Desktop and JalviewLite applet now
2554 require Java 1.5</li>
2555 <li>Allow Jalview feature colour specification for GFF
2556 sequence annotation files</li>
2557 <li>New 'colour by label' keword in Jalview feature file
2558 type colour specification</li>
2559 <li>New Jalview Desktop Groovy API method that allows a
2560 script to check if it being run in an interactive session or
2561 in a batch operation from the Jalview command line</li>
2565 <li>clustalx colourscheme colours Ds preferentially when
2566 both D+E are present in over 50% of the column</li>
2567 </ul> <em>Application</em>
2569 <li>typo in AlignmentFrame->View->Hide->all but
2570 selected Regions menu item</li>
2571 <li>sequence fetcher replaces ',' for ';' when the ',' is
2572 part of a valid accession ID</li>
2573 <li>fatal OOM if object retrieved by sequence fetcher
2574 runs out of memory</li>
2575 <li>unhandled Out of Memory Error when viewing pca
2576 analysis results</li>
2577 <li>InstallAnywhere builds fail to launch on OS X java
2578 10.5 update 4 (due to apple Java 1.6 update)</li>
2579 <li>Installanywhere Jalview silently fails to launch</li>
2580 </ul> <em>Applet</em>
2582 <li>Jalview.getFeatureGroups() raises an
2583 ArrayIndexOutOfBoundsException if no feature groups are
2590 <div align="center">
2591 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2597 <li>Alignment prettyprinter doesn't cope with long
2599 <li>clustalx colourscheme colours Ds preferentially when
2600 both D+E are present in over 50% of the column</li>
2601 <li>nucleic acid structures retrieved from PDB do not
2602 import correctly</li>
2603 <li>More columns get selected than were clicked on when a
2604 number of columns are hidden</li>
2605 <li>annotation label popup menu not providing correct
2606 add/hide/show options when rows are hidden or none are
2608 <li>Stockholm format shown in list of readable formats,
2609 and parser copes better with alignments from RFAM.</li>
2610 <li>CSV output of consensus only includes the percentage
2611 of all symbols if sequence logo display is enabled</li>
2613 </ul> <em>Applet</em>
2615 <li>annotation panel disappears when annotation is
2617 </ul> <em>Application</em>
2619 <li>Alignment view not redrawn properly when new
2620 alignment opened where annotation panel is visible but no
2621 annotations are present on alignment</li>
2622 <li>pasted region containing hidden columns is
2623 incorrectly displayed in new alignment window</li>
2624 <li>Jalview slow to complete operations when stdout is
2625 flooded (fix is to close the Jalview console)</li>
2626 <li>typo in AlignmentFrame->View->Hide->all but
2627 selected Rregions menu item.</li>
2628 <li>inconsistent group submenu and Format submenu entry
2629 'Un' or 'Non'conserved</li>
2630 <li>Sequence feature settings are being shared by
2631 multiple distinct alignments</li>
2632 <li>group annotation not recreated when tree partition is
2634 <li>double click on group annotation to select sequences
2635 does not propagate to associated trees</li>
2636 <li>Mac OSX specific issues:
2638 <li>exception raised when mouse clicked on desktop
2639 window background</li>
2640 <li>Desktop menu placed on menu bar and application
2641 name set correctly</li>
2642 <li>sequence feature settings not wide enough for the
2643 save feature colourscheme button</li>
2652 <div align="center">
2653 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2656 <td><em>New Capabilities</em>
2658 <li>URL links generated from description line for
2659 regular-expression based URL links (applet and application)
2661 <li>Non-positional feature URL links are shown in link
2663 <li>Linked viewing of nucleic acid sequences and
2665 <li>Automatic Scrolling option in View menu to display
2666 the currently highlighted region of an alignment.</li>
2667 <li>Order an alignment by sequence length, or using the
2668 average score or total feature count for each sequence.</li>
2669 <li>Shading features by score or associated description</li>
2670 <li>Subdivide alignment and groups based on identity of
2671 selected subsequence (Make Groups from Selection).</li>
2672 <li>New hide/show options including Shift+Control+H to
2673 hide everything but the currently selected region.</li>
2674 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2675 </ul> <em>Application</em>
2677 <li>Fetch DB References capabilities and UI expanded to
2678 support retrieval from DAS sequence sources</li>
2679 <li>Local DAS Sequence sources can be added via the
2680 command line or via the Add local source dialog box.</li>
2681 <li>DAS Dbref and DbxRef feature types are parsed as
2682 database references and protein_name is parsed as
2683 description line (BioSapiens terms).</li>
2684 <li>Enable or disable non-positional feature and database
2685 references in sequence ID tooltip from View menu in
2687 <!-- <li>New hidden columns and rows and representatives capabilities
2688 in annotations file (in progress - not yet fully implemented)</li> -->
2689 <li>Group-associated consensus, sequence logos and
2690 conservation plots</li>
2691 <li>Symbol distributions for each column can be exported
2692 and visualized as sequence logos</li>
2693 <li>Optionally scale multi-character column labels to fit
2694 within each column of annotation row<!-- todo for applet -->
2696 <li>Optional automatic sort of associated alignment view
2697 when a new tree is opened.</li>
2698 <li>Jalview Java Console</li>
2699 <li>Better placement of desktop window when moving
2700 between different screens.</li>
2701 <li>New preference items for sequence ID tooltip and
2702 consensus annotation</li>
2703 <li>Client to submit sequences and IDs to Envision2
2705 <li><em>Vamsas Capabilities</em>
2707 <li>Improved VAMSAS synchronization (Jalview archive
2708 used to preserve views, structures, and tree display
2710 <li>Import of vamsas documents from disk or URL via
2712 <li>Sharing of selected regions between views and
2713 with other VAMSAS applications (Experimental feature!)</li>
2714 <li>Updated API to VAMSAS version 0.2</li>
2716 </ul> <em>Applet</em>
2718 <li>Middle button resizes annotation row height</li>
2721 <li>sortByTree (true/false) - automatically sort the
2722 associated alignment view by the tree when a new tree is
2724 <li>showTreeBootstraps (true/false) - show or hide
2725 branch bootstraps (default is to show them if available)</li>
2726 <li>showTreeDistances (true/false) - show or hide
2727 branch lengths (default is to show them if available)</li>
2728 <li>showUnlinkedTreeNodes (true/false) - indicate if
2729 unassociated nodes should be highlighted in the tree
2731 <li>heightScale and widthScale (1.0 or more) -
2732 increase the height or width of a cell in the alignment
2733 grid relative to the current font size.</li>
2736 <li>Non-positional features displayed in sequence ID
2738 </ul> <em>Other</em>
2740 <li>Features format: graduated colour definitions and
2741 specification of feature scores</li>
2742 <li>Alignment Annotations format: new keywords for group
2743 associated annotation (GROUP_REF) and annotation row display
2744 properties (ROW_PROPERTIES)</li>
2745 <li>XML formats extended to support graduated feature
2746 colourschemes, group associated annotation, and profile
2747 visualization settings.</li></td>
2750 <li>Source field in GFF files parsed as feature source
2751 rather than description</li>
2752 <li>Non-positional features are now included in sequence
2753 feature and gff files (controlled via non-positional feature
2754 visibility in tooltip).</li>
2755 <li>URL links generated for all feature links (bugfix)</li>
2756 <li>Added URL embedding instructions to features file
2758 <li>Codons containing ambiguous nucleotides translated as
2759 'X' in peptide product</li>
2760 <li>Match case switch in find dialog box works for both
2761 sequence ID and sequence string and query strings do not
2762 have to be in upper case to match case-insensitively.</li>
2763 <li>AMSA files only contain first column of
2764 multi-character column annotation labels</li>
2765 <li>Jalview Annotation File generation/parsing consistent
2766 with documentation (e.g. Stockholm annotation can be
2767 exported and re-imported)</li>
2768 <li>PDB files without embedded PDB IDs given a friendly
2770 <li>Find incrementally searches ID string matches as well
2771 as subsequence matches, and correctly reports total number
2775 <li>Better handling of exceptions during sequence
2777 <li>Dasobert generated non-positional feature URL
2778 link text excludes the start_end suffix</li>
2779 <li>DAS feature and source retrieval buttons disabled
2780 when fetch or registry operations in progress.</li>
2781 <li>PDB files retrieved from URLs are cached properly</li>
2782 <li>Sequence description lines properly shared via
2784 <li>Sequence fetcher fetches multiple records for all
2786 <li>Ensured that command line das feature retrieval
2787 completes before alignment figures are generated.</li>
2788 <li>Reduced time taken when opening file browser for
2790 <li>isAligned check prior to calculating tree, PCA or
2791 submitting an MSA to JNet now excludes hidden sequences.</li>
2792 <li>User defined group colours properly recovered
2793 from Jalview projects.</li>
2802 <div align="center">
2803 <strong>2.4.0.b2</strong><br> 28/10/2009
2808 <li>Experimental support for google analytics usage
2810 <li>Jalview privacy settings (user preferences and docs).</li>
2815 <li>Race condition in applet preventing startup in
2817 <li>Exception when feature created from selection beyond
2818 length of sequence.</li>
2819 <li>Allow synthetic PDB files to be imported gracefully</li>
2820 <li>Sequence associated annotation rows associate with
2821 all sequences with a given id</li>
2822 <li>Find function matches case-insensitively for sequence
2823 ID string searches</li>
2824 <li>Non-standard characters do not cause pairwise
2825 alignment to fail with exception</li>
2826 </ul> <em>Application Issues</em>
2828 <li>Sequences are now validated against EMBL database</li>
2829 <li>Sequence fetcher fetches multiple records for all
2831 </ul> <em>InstallAnywhere Issues</em>
2833 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2834 issue with installAnywhere mechanism)</li>
2835 <li>Command line launching of JARs from InstallAnywhere
2836 version (java class versioning error fixed)</li>
2843 <div align="center">
2844 <strong>2.4</strong><br> 27/8/2008
2847 <td><em>User Interface</em>
2849 <li>Linked highlighting of codon and amino acid from
2850 translation and protein products</li>
2851 <li>Linked highlighting of structure associated with
2852 residue mapping to codon position</li>
2853 <li>Sequence Fetcher provides example accession numbers
2854 and 'clear' button</li>
2855 <li>MemoryMonitor added as an option under Desktop's
2857 <li>Extract score function to parse whitespace separated
2858 numeric data in description line</li>
2859 <li>Column labels in alignment annotation can be centred.</li>
2860 <li>Tooltip for sequence associated annotation give name
2862 </ul> <em>Web Services and URL fetching</em>
2864 <li>JPred3 web service</li>
2865 <li>Prototype sequence search client (no public services
2867 <li>Fetch either seed alignment or full alignment from
2869 <li>URL Links created for matching database cross
2870 references as well as sequence ID</li>
2871 <li>URL Links can be created using regular-expressions</li>
2872 </ul> <em>Sequence Database Connectivity</em>
2874 <li>Retrieval of cross-referenced sequences from other
2876 <li>Generalised database reference retrieval and
2877 validation to all fetchable databases</li>
2878 <li>Fetch sequences from DAS sources supporting the
2879 sequence command</li>
2880 </ul> <em>Import and Export</em>
2881 <li>export annotation rows as CSV for spreadsheet import</li>
2882 <li>Jalview projects record alignment dataset associations,
2883 EMBL products, and cDNA sequence mappings</li>
2884 <li>Sequence Group colour can be specified in Annotation
2886 <li>Ad-hoc colouring of group in Annotation File using RGB
2887 triplet as name of colourscheme</li>
2888 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2890 <li>treenode binding for VAMSAS tree exchange</li>
2891 <li>local editing and update of sequences in VAMSAS
2892 alignments (experimental)</li>
2893 <li>Create new or select existing session to join</li>
2894 <li>load and save of vamsas documents</li>
2895 </ul> <em>Application command line</em>
2897 <li>-tree parameter to open trees (introduced for passing
2899 <li>-fetchfrom command line argument to specify nicknames
2900 of DAS servers to query for alignment features</li>
2901 <li>-dasserver command line argument to add new servers
2902 that are also automatically queried for features</li>
2903 <li>-groovy command line argument executes a given groovy
2904 script after all input data has been loaded and parsed</li>
2905 </ul> <em>Applet-Application data exchange</em>
2907 <li>Trees passed as applet parameters can be passed to
2908 application (when using "View in full
2909 application")</li>
2910 </ul> <em>Applet Parameters</em>
2912 <li>feature group display control parameter</li>
2913 <li>debug parameter</li>
2914 <li>showbutton parameter</li>
2915 </ul> <em>Applet API methods</em>
2917 <li>newView public method</li>
2918 <li>Window (current view) specific get/set public methods</li>
2919 <li>Feature display control methods</li>
2920 <li>get list of currently selected sequences</li>
2921 </ul> <em>New Jalview distribution features</em>
2923 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2924 <li>RELEASE file gives build properties for the latest
2925 Jalview release.</li>
2926 <li>Java 1.1 Applet build made easier and donotobfuscate
2927 property controls execution of obfuscator</li>
2928 <li>Build target for generating source distribution</li>
2929 <li>Debug flag for javacc</li>
2930 <li>.jalview_properties file is documented (slightly) in
2931 jalview.bin.Cache</li>
2932 <li>Continuous Build Integration for stable and
2933 development version of Application, Applet and source
2938 <li>selected region output includes visible annotations
2939 (for certain formats)</li>
2940 <li>edit label/displaychar contains existing label/char
2942 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2943 <li>shorter peptide product names from EMBL records</li>
2944 <li>Newick string generator makes compact representations</li>
2945 <li>bootstrap values parsed correctly for tree files with
2947 <li>pathological filechooser bug avoided by not allowing
2948 filenames containing a ':'</li>
2949 <li>Fixed exception when parsing GFF files containing
2950 global sequence features</li>
2951 <li>Alignment datasets are finalized only when number of
2952 references from alignment sequences goes to zero</li>
2953 <li>Close of tree branch colour box without colour
2954 selection causes cascading exceptions</li>
2955 <li>occasional negative imgwidth exceptions</li>
2956 <li>better reporting of non-fatal warnings to user when
2957 file parsing fails.</li>
2958 <li>Save works when Jalview project is default format</li>
2959 <li>Save as dialog opened if current alignment format is
2960 not a valid output format</li>
2961 <li>UniProt canonical names introduced for both das and
2963 <li>Histidine should be midblue (not pink!) in Zappo</li>
2964 <li>error messages passed up and output when data read
2966 <li>edit undo recovers previous dataset sequence when
2967 sequence is edited</li>
2968 <li>allow PDB files without pdb ID HEADER lines (like
2969 those generated by MODELLER) to be read in properly</li>
2970 <li>allow reading of JPred concise files as a normal
2972 <li>Stockholm annotation parsing and alignment properties
2973 import fixed for PFAM records</li>
2974 <li>Structure view windows have correct name in Desktop
2976 <li>annotation consisting of sequence associated scores
2977 can be read and written correctly to annotation file</li>
2978 <li>Aligned cDNA translation to aligned peptide works
2980 <li>Fixed display of hidden sequence markers and
2981 non-italic font for representatives in Applet</li>
2982 <li>Applet Menus are always embedded in applet window on
2984 <li>Newly shown features appear at top of stack (in
2986 <li>Annotations added via parameter not drawn properly
2987 due to null pointer exceptions</li>
2988 <li>Secondary structure lines are drawn starting from
2989 first column of alignment</li>
2990 <li>UniProt XML import updated for new schema release in
2992 <li>Sequence feature to sequence ID match for Features
2993 file is case-insensitive</li>
2994 <li>Sequence features read from Features file appended to
2995 all sequences with matching IDs</li>
2996 <li>PDB structure coloured correctly for associated views
2997 containing a sub-sequence</li>
2998 <li>PDB files can be retrieved by applet from Jar files</li>
2999 <li>feature and annotation file applet parameters
3000 referring to different directories are retrieved correctly</li>
3001 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
3002 <li>Fixed application hang whilst waiting for
3003 splash-screen version check to complete</li>
3004 <li>Applet properly URLencodes input parameter values
3005 when passing them to the launchApp service</li>
3006 <li>display name and local features preserved in results
3007 retrieved from web service</li>
3008 <li>Visual delay indication for sequence retrieval and
3009 sequence fetcher initialisation</li>
3010 <li>updated Application to use DAS 1.53e version of
3011 dasobert DAS client</li>
3012 <li>Re-instated Full AMSA support and .amsa file
3014 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
3022 <div align="center">
3023 <strong>2.3</strong><br> 9/5/07
3028 <li>Jmol 11.0.2 integration</li>
3029 <li>PDB views stored in Jalview XML files</li>
3030 <li>Slide sequences</li>
3031 <li>Edit sequence in place</li>
3032 <li>EMBL CDS features</li>
3033 <li>DAS Feature mapping</li>
3034 <li>Feature ordering</li>
3035 <li>Alignment Properties</li>
3036 <li>Annotation Scores</li>
3037 <li>Sort by scores</li>
3038 <li>Feature/annotation editing in applet</li>
3043 <li>Headless state operation in 2.2.1</li>
3044 <li>Incorrect and unstable DNA pairwise alignment</li>
3045 <li>Cut and paste of sequences with annotation</li>
3046 <li>Feature group display state in XML</li>
3047 <li>Feature ordering in XML</li>
3048 <li>blc file iteration selection using filename # suffix</li>
3049 <li>Stockholm alignment properties</li>
3050 <li>Stockhom alignment secondary structure annotation</li>
3051 <li>2.2.1 applet had no feature transparency</li>
3052 <li>Number pad keys can be used in cursor mode</li>
3053 <li>Structure Viewer mirror image resolved</li>
3060 <div align="center">
3061 <strong>2.2.1</strong><br> 12/2/07
3066 <li>Non standard characters can be read and displayed
3067 <li>Annotations/Features can be imported/exported to the
3069 <li>Applet allows editing of sequence/annotation/group
3070 name & description
3071 <li>Preference setting to display sequence name in
3073 <li>Annotation file format extended to allow
3074 Sequence_groups to be defined
3075 <li>Default opening of alignment overview panel can be
3076 specified in preferences
3077 <li>PDB residue numbering annotation added to associated
3083 <li>Applet crash under certain Linux OS with Java 1.6
3085 <li>Annotation file export / import bugs fixed
3086 <li>PNG / EPS image output bugs fixed
3092 <div align="center">
3093 <strong>2.2</strong><br> 27/11/06
3098 <li>Multiple views on alignment
3099 <li>Sequence feature editing
3100 <li>"Reload" alignment
3101 <li>"Save" to current filename
3102 <li>Background dependent text colour
3103 <li>Right align sequence ids
3104 <li>User-defined lower case residue colours
3107 <li>Menu item accelerator keys
3108 <li>Control-V pastes to current alignment
3109 <li>Cancel button for DAS Feature Fetching
3110 <li>PCA and PDB Viewers zoom via mouse roller
3111 <li>User-defined sub-tree colours and sub-tree selection
3113 <li>'New Window' button on the 'Output to Text box'
3118 <li>New memory efficient Undo/Redo System
3119 <li>Optimised symbol lookups and conservation/consensus
3121 <li>Region Conservation/Consensus recalculated after
3123 <li>Fixed Remove Empty Columns Bug (empty columns at end
3125 <li>Slowed DAS Feature Fetching for increased robustness.
3127 <li>Made angle brackets in ASCII feature descriptions
3129 <li>Re-instated Zoom function for PCA
3130 <li>Sequence descriptions conserved in web service
3132 <li>UniProt ID discoverer uses any word separated by
3134 <li>WsDbFetch query/result association resolved
3135 <li>Tree leaf to sequence mapping improved
3136 <li>Smooth fonts switch moved to FontChooser dialog box.
3143 <div align="center">
3144 <strong>2.1.1</strong><br> 12/9/06
3149 <li>Copy consensus sequence to clipboard</li>
3154 <li>Image output - rightmost residues are rendered if
3155 sequence id panel has been resized</li>
3156 <li>Image output - all offscreen group boundaries are
3158 <li>Annotation files with sequence references - all
3159 elements in file are relative to sequence position</li>
3160 <li>Mac Applet users can use Alt key for group editing</li>
3166 <div align="center">
3167 <strong>2.1</strong><br> 22/8/06
3172 <li>MAFFT Multiple Alignment in default Web Service list</li>
3173 <li>DAS Feature fetching</li>
3174 <li>Hide sequences and columns</li>
3175 <li>Export Annotations and Features</li>
3176 <li>GFF file reading / writing</li>
3177 <li>Associate structures with sequences from local PDB
3179 <li>Add sequences to exisiting alignment</li>
3180 <li>Recently opened files / URL lists</li>
3181 <li>Applet can launch the full application</li>
3182 <li>Applet has transparency for features (Java 1.2
3184 <li>Applet has user defined colours parameter</li>
3185 <li>Applet can load sequences from parameter
3186 "sequence<em>x</em>"
3192 <li>Redundancy Panel reinstalled in the Applet</li>
3193 <li>Monospaced font - EPS / rescaling bug fixed</li>
3194 <li>Annotation files with sequence references bug fixed</li>
3200 <div align="center">
3201 <strong>2.08.1</strong><br> 2/5/06
3206 <li>Change case of selected region from Popup menu</li>
3207 <li>Choose to match case when searching</li>
3208 <li>Middle mouse button and mouse movement can compress /
3209 expand the visible width and height of the alignment</li>
3214 <li>Annotation Panel displays complete JNet results</li>
3220 <div align="center">
3221 <strong>2.08b</strong><br> 18/4/06
3227 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3228 <li>Righthand label on wrapped alignments shows correct
3235 <div align="center">
3236 <strong>2.08</strong><br> 10/4/06
3241 <li>Editing can be locked to the selection area</li>
3242 <li>Keyboard editing</li>
3243 <li>Create sequence features from searches</li>
3244 <li>Precalculated annotations can be loaded onto
3246 <li>Features file allows grouping of features</li>
3247 <li>Annotation Colouring scheme added</li>
3248 <li>Smooth fonts off by default - Faster rendering</li>
3249 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3254 <li>Drag & Drop fixed on Linux</li>
3255 <li>Jalview Archive file faster to load/save, sequence
3256 descriptions saved.</li>
3262 <div align="center">
3263 <strong>2.07</strong><br> 12/12/05
3268 <li>PDB Structure Viewer enhanced</li>
3269 <li>Sequence Feature retrieval and display enhanced</li>
3270 <li>Choose to output sequence start-end after sequence
3271 name for file output</li>
3272 <li>Sequence Fetcher WSDBFetch@EBI</li>
3273 <li>Applet can read feature files, PDB files and can be
3274 used for HTML form input</li>
3279 <li>HTML output writes groups and features</li>
3280 <li>Group editing is Control and mouse click</li>
3281 <li>File IO bugs</li>
3287 <div align="center">
3288 <strong>2.06</strong><br> 28/9/05
3293 <li>View annotations in wrapped mode</li>
3294 <li>More options for PCA viewer</li>
3299 <li>GUI bugs resolved</li>
3300 <li>Runs with -nodisplay from command line</li>
3306 <div align="center">
3307 <strong>2.05b</strong><br> 15/9/05
3312 <li>Choose EPS export as lineart or text</li>
3313 <li>Jar files are executable</li>
3314 <li>Can read in Uracil - maps to unknown residue</li>
3319 <li>Known OutOfMemory errors give warning message</li>
3320 <li>Overview window calculated more efficiently</li>
3321 <li>Several GUI bugs resolved</li>
3327 <div align="center">
3328 <strong>2.05</strong><br> 30/8/05
3333 <li>Edit and annotate in "Wrapped" view</li>
3338 <li>Several GUI bugs resolved</li>
3344 <div align="center">
3345 <strong>2.04</strong><br> 24/8/05
3350 <li>Hold down mouse wheel & scroll to change font
3356 <li>Improved JPred client reliability</li>
3357 <li>Improved loading of Jalview files</li>
3363 <div align="center">
3364 <strong>2.03</strong><br> 18/8/05
3369 <li>Set Proxy server name and port in preferences</li>
3370 <li>Multiple URL links from sequence ids</li>
3371 <li>User Defined Colours can have a scheme name and added
3373 <li>Choose to ignore gaps in consensus calculation</li>
3374 <li>Unix users can set default web browser</li>
3375 <li>Runs without GUI for batch processing</li>
3376 <li>Dynamically generated Web Service Menus</li>
3381 <li>InstallAnywhere download for Sparc Solaris</li>
3387 <div align="center">
3388 <strong>2.02</strong><br> 18/7/05
3394 <li>Copy & Paste order of sequences maintains
3395 alignment order.</li>
3401 <div align="center">
3402 <strong>2.01</strong><br> 12/7/05
3407 <li>Use delete key for deleting selection.</li>
3408 <li>Use Mouse wheel to scroll sequences.</li>
3409 <li>Help file updated to describe how to add alignment
3411 <li>Version and build date written to build properties
3413 <li>InstallAnywhere installation will check for updates
3414 at launch of Jalview.</li>
3419 <li>Delete gaps bug fixed.</li>
3420 <li>FileChooser sorts columns.</li>
3421 <li>Can remove groups one by one.</li>
3422 <li>Filechooser icons installed.</li>
3423 <li>Finder ignores return character when searching.
3424 Return key will initiate a search.<br>
3431 <div align="center">
3432 <strong>2.0</strong><br> 20/6/05
3437 <li>New codebase</li>