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>
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27 list-style-type: none;
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50 <strong>Release History</strong>
54 <td width="60" nowrap>
56 <em><strong>Release</strong></em>
61 <em><strong>New Features</strong></em>
66 <em><strong>Issues Resolved</strong></em>
71 <td width="60" nowrap>
73 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>8/8/2017</em></strong>
76 <td><div align="left">
81 <!-- JAL-1933 -->Occupancy annotation row shows number of
82 ungapped positions in each column of the alignment.
85 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
86 a calculation dialog box
89 <!-- JAL-2379 -->Revised implementation of PCA for speed
90 and memory efficiency (~30x faster)
93 <!-- JAL-2403 -->Revised implementation of sequence
94 similarity scores as used by Tree, PCA, Shading Consensus
95 and other calculations
98 <!-- JAL-2416 -->Score matrices are stored as resource
99 files within the Jalview codebase
102 <!-- JAL-2500 -->Trees computed on Sequence Feature
103 Similarity may have different topology due to increased
110 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
111 model for alignments and groups
114 <!-- JAL-384 -->Custom shading schemes created via groovy
121 <!-- JAL-2526 -->Efficiency improvements for interacting
122 with alignment and overview windows
125 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
126 via Overview or sequence motif search operations
129 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
133 <!-- JAL-2388 -->Hidden columns and sequences can be
137 <!-- JAL-2611 -->Click-drag in visible area allows fine
138 adjustment of visible position
142 <em>Data import/export</em>
145 <!-- JAL-2535 -->Posterior probability annotation from
146 Stockholm files imported as sequence associated annotation
149 <!-- JAL-2507 -->More robust per-sequence positional
150 annotation input/output via stockholm flatfile
153 <!-- JAL-2533 -->Sequence names don't include file
154 extension when importing structure files without embedded
155 names or PDB accessions
158 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
159 format sequence substitution matrices
162 <em>User Interface</em>
165 <!-- JAL-2447 --> Experimental Features Checkbox in
166 Desktop's Tools menu to hide or show untested features in
170 <!-- JAL-2547 -->Amend sequence features dialog box can be
171 opened by double clicking gaps within sequence feature
175 <!-- JAL-1476 -->Status bar message shown when not enough
176 aligned positions were available to create a 3D structure
180 <em>3D Structure</em>
183 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
184 file-based command exchange
187 <!-- JAL-2375 -->Structure chooser automatically shows
188 Cached Structures rather than querying the PDBe if
189 structures are already available for sequences
192 <!-- JAL-2520 -->Structures imported via URL are cached in
193 the Jalview project rather than downloaded again when the
197 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
198 to transfer Chimera's structure attributes as Jalview
199 features, and vice-versa (<strong>Experimental
203 <em>Web Services</em>
206 <!-- JAL-2549 -->Updated JABAWS client to v2.2
209 <!-- JAL-2316, -->URLs for viewing database
210 cross-references provided by identifiers.org and the
218 <!-- JAL-2344 -->FileFormatI interface for describing and
219 identifying file formats (instead of String constants)
222 <!-- JAL-2228 -->FeatureCounter script refactored for
223 efficiency when counting all displayed features (not
224 backwards compatible with 2.10.1)
227 <em>Example files</em>
230 <!-- JAL-2631 -->Graduated feature colour style example
231 included in the example feature file
234 <em>Documentation</em>
237 <!-- JAL-2339 -->Release notes reformatted for readibility
238 with the built-in Java help viewer
241 <!-- JAL-1644 -->Find documentation updated with 'search
242 sequence description' option
248 <!-- JAL-2485, -->External service integration tests for
249 Uniprot REST Free Text Search Client
252 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
255 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
260 <td><div align="left">
261 <em>Calculations</em>
264 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
265 matrix - C->R should be '-3'<br />Old matrix restored
266 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
269 <!-- JAL-2397 -->Fixed Jalview's treatment of gaps in PCA
270 and substitution matrix based Tree calculations.<br />In
271 earlier versions of Jalview, gaps matching gaps were
272 penalised, and gaps matching non-gaps penalised even more.
273 In the PCA calculation, gaps were actually treated as
274 non-gaps - so different costs were applied, which meant
275 Jalview's PCAs were different to those produced by
276 SeqSpace.<br />Jalview now treats gaps in the same way as
277 SeqSpace (ie it scores them as 0). To restore pre-2.10.2
279 jalview.viewmodel.PCAModel.scoreGapAsAny=true // for
281 jalview.viewmodel.PCAModel.scoreGapAsAny=false // to
285 <!-- JAL-2424 -->Fixed off-by-one bug that affected
286 scaling of branch lengths for trees computed using
287 Sequence Feature Similarity.
290 <!-- JAL-2377 -->PCA calculation could hang when
291 generating output report when working with highly
295 <!-- JAL-2544 --> Sort by features includes features to
296 right of selected region when gaps present on right-hand
300 <em>User Interface</em>
303 <!-- JAL-2346 -->Reopening Colour by annotation dialog
304 doesn't reselect a specific sequence's associated
305 annotation after it was used for colouring a view
308 <!-- JAL-2419 -->Current selection lost if popup menu
309 opened on a region of alignment without groups
312 <!-- JAL-2374 -->Popup menu not always shown for regions
313 of an alignment with overlapping groups
316 <!-- JAL-2310 -->Finder double counts if both a sequence's
317 name and description match
320 <!-- JAL-2370 -->Hiding column selection containing two
321 hidden regions results in incorrect hidden regions
324 <!-- JAL-2386 -->'Apply to all groups' setting when
325 changing colour does not apply Conservation slider value
329 <!-- JAL-2373 -->Percentage identity and conservation menu
330 items do not show a tick or allow shading to be disabled
333 <!-- JAL-2385 -->Conservation shading or PID threshold
334 lost when base colourscheme changed if slider not visible
337 <!-- JAL-2547 -->Sequence features shown in tooltip for
338 gaps before start of features
341 <!-- JAL-2623 -->Graduated feature colour threshold not
342 restored to UI when feature colour is edited
345 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
346 a time when scrolling vertically in wrapped mode.
349 <!-- JAL-2630 -->Structure and alignment overview update
350 as graduate feature colour settings are modified via the
354 <!-- JAL-2034 -->Overview window doesn't always update
355 when a group defined on the alignment is resized
358 <!-- JAL-2605 -->Mouseovers on left/right scale region in
359 wrapped view result in positional status updates
363 <!-- JAL-2563 -->Status bar doesn't show position for
364 ambiguous amino acid and nucleotide symbols
367 <!-- JAL-2602 -->Copy consensus sequence failed if
368 alignment included gapped columns
371 <!-- JAL-2473 -->Minimum size set for Jalview windows so
372 widgets don't permanently disappear
375 <!-- JAL-2503 -->Cannot select or filter quantitative
376 annotation that are shown only as column labels (e.g.
377 T-Coffee column reliability scores)
380 <!-- JAL-2594 -->Exception thrown if trying to create a
381 sequence feature on gaps only
384 <!-- JAL-2504 -->Features created with 'New feature'
385 button from a Find inherit previously defined feature type
386 rather than the Find query string
389 <!-- JAL-2423 -->incorrect title in output window when
390 exporting tree calculated in Jalview
393 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
394 and then revealing them reorders sequences on the
398 <!-- JAL-964 -->Group panel in sequence feature settings
399 doesn't update to reflect available set of groups after
400 interactively adding or modifying features
403 <!-- JAL-2225 -->Sequence Database chooser unusable on
407 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
408 only excluded gaps in current sequence and ignored
415 <!-- JAL-2430 -->Hidden regions in alignment views are not
416 coloured in linked structure views
419 <!-- JAL-2421 -->Overview window visible region moves
420 erratically when hidden rows or columns are present
423 <!-- JAL-2362 -->Per-residue colourschemes applied via the
424 Structure Viewer's colour menu don't correspond to
428 <!-- JAL-2405 -->Protein specific colours only offered in
429 colour and group colour menu for protein alignments
432 <!-- JAL-2385 -->Colour threshold slider doesn't update to
433 reflect currently selected view or group's shading
437 <!-- JAL-2624 -->Feature colour thresholds not respected
438 when rendered on overview and structures when opacity at
442 <!-- JAL-2589 -->User defined gap colour not shown in
443 overview when features overlaid on alignment
446 <em>Data import/export</em>
449 <!-- JAL-2576 -->Very large alignments take a long time to
453 <!-- JAL-2507 -->Per-sequence RNA secondary structures
454 added after a sequence was imported are not written to
458 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
459 when importing RNA secondary structure via Stockholm
462 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
463 not shown in correct direction for simple pseudoknots
466 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
467 with lightGray or darkGray via features file (but can
471 <!-- JAL-2383 -->Above PID colour threshold not recovered
472 when alignment view imported from project
475 <!-- JAL-2520,JAL-2465 -->No mappings generated between
476 structure and sequences extracted from structure files
477 imported via URL and viewed in Jmol
480 <!-- JAL-2520 -->Structures loaded via URL are saved in
481 Jalview Projects rather than fetched via URL again when
482 the project is loaded and the structure viewed
485 <em>Web Services</em>
488 <!-- JAL-2519 -->EnsemblGenomes example failing after
489 release of Ensembl v.88
492 <!-- JAL-2366 -->Proxy server address and port always
493 appear enabled in Preferences->Connections
496 <!-- JAL-2461 -->DAS registry not found exceptions
497 removed from console output
500 <!-- JAL-2582 -->Cannot retrieve protein products from
501 Ensembl by Peptide ID
504 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
505 created from SIFTs, and spurious 'Couldn't open structure
506 in Chimera' errors raised after April 2017 update (problem
507 due to 'null' string rather than empty string used for
508 residues with no corresponding PDB mapping).
511 <em>Application UI</em>
514 <!-- JAL-2361 -->User Defined Colours not added to Colour
518 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
519 case' residues (button in colourscheme editor debugged and
520 new documentation and tooltips added)
523 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
524 doesn't restore group-specific text colour thresholds
527 <!-- JAL-2243 -->Feature settings panel does not update as
528 new features are added to alignment
531 <!-- JAL-2532 -->Cancel in feature settings reverts
532 changes to feature colours via the Amend features dialog
535 <!-- JAL-2506 -->Null pointer exception when attempting to
536 edit graduated feature colour via amend features dialog
540 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
541 selection menu changes colours of alignment views
544 <!-- JAL-2426 -->Spurious exceptions in console raised
545 from alignment calculation workers after alignment has
549 <!-- JAL-1608 -->Typo in selection popup menu - Create
550 groups now 'Create Group'
553 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
554 Create/Undefine group doesn't always work
557 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
558 shown again after pressing 'Cancel'
561 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
562 adjusts start position in wrap mode
565 <!-- JAL-2563 -->Status bar doesn't show positions for
566 ambiguous amino acids
569 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
570 CDS/Protein view after CDS sequences added for aligned
574 <!-- JAL-2592 -->User defined colourschemes called 'User
575 Defined' don't appear in Colours menu
581 <!-- JAL-2468 -->Switching between Nucleotide and Protein
582 score models doesn't always result in an updated PCA plot
585 <!-- JAL-2442 -->Features not rendered as transparent on
586 overview or linked structure view
589 <!-- JAL-2372 -->Colour group by conservation doesn't
593 <!-- JAL-2517 -->Hitting Cancel after applying
594 user-defined colourscheme doesn't restore original
601 <!-- JAL-2314 -->Unit test failure:
602 jalview.ws.jabaws.RNAStructExportImport setup fails
605 <!-- JAL-2307 -->Unit test failure:
606 jalview.ws.sifts.SiftsClientTest due to compatibility
607 problems with deep array comparison equality asserts in
608 successive versions of TestNG
611 <!-- JAL-2479 -->Relocated StructureChooserTest and
612 ParameterUtilsTest Unit tests to Network suite
615 <em>New Known Issues</em>
618 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
619 phase after a sequence motif find operation
622 <!-- JAL-2550 -->Importing annotation file with rows
623 containing just upper and lower case letters are
624 interpreted as WUSS rna secondary structure symbols
627 <!-- JAL-2590 -->Cannot load Newick trees from eggnog
631 <!-- JAL-2468 -->Status bar shows 'Marked x columns
632 containing features of type Highlight' when 'B" is pressed
633 to mark columns containing highlighted regions.
637 <td width="60" nowrap>
639 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
642 <td><div align="left">
646 <!-- JAL-98 -->Improved memory usage: sparse arrays used
647 for all consensus calculations
650 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
653 <li>Updated Jalview's Certum code signing certificate
659 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
660 set of database cross-references, sorted alphabetically
663 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
664 from database cross references. Users with custom links
665 will receive a <a href="webServices/urllinks.html#warning">warning
666 dialog</a> asking them to update their preferences.
669 <!-- JAL-2287-->Cancel button and escape listener on
670 dialog warning user about disconnecting Jalview from a
674 <!-- JAL-2320-->Jalview's Chimera control window closes if
675 the Chimera it is connected to is shut down
678 <!-- JAL-1738-->New keystroke (B) and Select highlighted
679 columns menu item to mark columns containing highlighted
680 regions (e.g. from structure selections or results of a
684 <!-- JAL-2284-->Command line option for batch-generation
685 of HTML pages rendering alignment data with the BioJS
695 <!-- JAL-2286 -->Columns with more than one modal residue
696 are not coloured or thresholded according to percent
697 identity (first observed in Jalview 2.8.2)
700 <!-- JAL-2301 -->Threonine incorrectly reported as not
704 <!-- JAL-2318 -->Updates to documentation pages (above PID
705 threshold, amino acid properties)
708 <!-- JAL-2292 -->Lower case residues in sequences are not
709 reported as mapped to residues in a structure file in the
713 <!--JAL-2324 -->Identical features with non-numeric scores
714 could be added multiple times to a sequence
717 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
718 bond features shown as two highlighted residues rather
719 than a range in linked structure views, and treated
720 correctly when selecting and computing trees from features
723 <!-- JAL-2281-->Custom URL links for database
724 cross-references are matched to database name regardless
732 <!-- JAL-2282-->Custom URL links for specific database
733 names without regular expressions also offer links from
737 <!-- JAL-2315-->Removing a single configured link in the
738 URL links pane in Connections preferences doesn't actually
739 update Jalview configuration
742 <!-- JAL-2272-->CTRL-Click on a selected region to open
743 the alignment area popup menu doesn't work on El-Capitan
746 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
747 files with similarly named sequences if dropped onto the
751 <!-- JAL-2312 -->Additional mappings are shown for PDB
752 entries where more chains exist in the PDB accession than
753 are reported in the SIFTS file
756 <!-- JAL-2317-->Certain structures do not get mapped to
757 the structure view when displayed with Chimera
760 <!-- JAL-2317-->No chains shown in the Chimera view
761 panel's View->Show Chains submenu
764 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
765 work for wrapped alignment views
768 <!--JAL-2197 -->Rename UI components for running JPred
769 predictions from 'JNet' to 'JPred'
772 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
773 corrupted when annotation panel vertical scroll is not at
777 <!--JAL-2332 -->Attempting to view structure for Hen
778 lysozyme results in a PDB Client error dialog box
781 <!-- JAL-2319 -->Structure View's mapping report switched
782 ranges for PDB and sequence for SIFTS
785 SIFTS 'Not_Observed' residues mapped to non-existant
789 <!-- <em>New Known Issues</em>
796 <td width="60" nowrap>
798 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
799 <em>25/10/2016</em></strong>
802 <td><em>Application</em>
804 <li>3D Structure chooser opens with 'Cached structures'
805 view if structures already loaded</li>
806 <li>Progress bar reports models as they are loaded to
813 <li>Colour by conservation always enabled and no tick
814 shown in menu when BLOSUM or PID shading applied</li>
815 <li>FER1_ARATH and FER2_ARATH labels were switched in
816 example sequences/projects/trees</li>
820 <li>Jalview projects with views of local PDB structure
821 files saved on Windows cannot be opened on OSX</li>
822 <li>Multiple structure views can be opened and superposed
823 without timeout for structures with multiple models or
824 multiple sequences in alignment</li>
825 <li>Cannot import or associated local PDB files without a
826 PDB ID HEADER line</li>
827 <li>RMSD is not output in Jmol console when superposition
829 <li>Drag and drop of URL from Browser fails for Linux and
830 OSX versions earlier than El Capitan</li>
831 <li>ENA client ignores invalid content from ENA server</li>
832 <li>Exceptions are not raised in console when ENA client
833 attempts to fetch non-existent IDs via Fetch DB Refs UI
835 <li>Exceptions are not raised in console when a new view
836 is created on the alignment</li>
837 <li>OSX right-click fixed for group selections: CMD-click
838 to insert/remove gaps in groups and CTRL-click to open group
841 <em>Build and deployment</em>
843 <li>URL link checker now copes with multi-line anchor
846 <em>New Known Issues</em>
848 <li>Drag and drop from URL links in browsers do not work
855 <td width="60" nowrap>
857 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
863 <!-- JAL-2124 -->Updated Spanish translations.
866 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
867 for importing structure data to Jalview. Enables mmCIF and
871 <!-- JAL-192 --->Alignment ruler shows positions relative to
875 <!-- JAL-2202 -->Position/residue shown in status bar when
876 mousing over sequence associated annotation
879 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
883 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
884 '()', canonical '[]' and invalid '{}' base pair populations
888 <!-- JAL-2092 -->Feature settings popup menu options for
889 showing or hiding columns containing a feature
892 <!-- JAL-1557 -->Edit selected group by double clicking on
893 group and sequence associated annotation labels
896 <!-- JAL-2236 -->Sequence name added to annotation label in
897 select/hide columns by annotation and colour by annotation
901 </ul> <em>Application</em>
904 <!-- JAL-2050-->Automatically hide introns when opening a
908 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
912 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
913 structure mappings with the EMBL-EBI PDBe SIFTS database
916 <!-- JAL-2079 -->Updated download sites used for Rfam and
917 Pfam sources to xfam.org
920 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
923 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
924 over sequences in Jalview
927 <!-- JAL-2027-->Support for reverse-complement coding
928 regions in ENA and EMBL
931 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
932 for record retrieval via ENA rest API
935 <!-- JAL-2027 -->Support for ENA CDS records with reverse
939 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
940 groovy script execution
943 <!-- JAL-1812 -->New 'execute Groovy script' option in an
944 alignment window's Calculate menu
947 <!-- JAL-1812 -->Allow groovy scripts that call
948 Jalview.getAlignFrames() to run in headless mode
951 <!-- JAL-2068 -->Support for creating new alignment
952 calculation workers from groovy scripts
955 <!-- JAL-1369 --->Store/restore reference sequence in
959 <!-- JAL-1803 -->Chain codes for a sequence's PDB
960 associations are now saved/restored from project
963 <!-- JAL-1993 -->Database selection dialog always shown
964 before sequence fetcher is opened
967 <!-- JAL-2183 -->Double click on an entry in Jalview's
968 database chooser opens a sequence fetcher
971 <!-- JAL-1563 -->Free-text search client for UniProt using
975 <!-- JAL-2168 -->-nonews command line parameter to prevent
976 the news reader opening
979 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
980 querying stored in preferences
983 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
987 <!-- JAL-1977-->Tooltips shown on database chooser
990 <!-- JAL-391 -->Reverse complement function in calculate
991 menu for nucleotide sequences
994 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
995 and feature counts preserves alignment ordering (and
996 debugged for complex feature sets).
999 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
1000 viewing structures with Jalview 2.10
1003 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
1004 genome, transcript CCDS and gene ids via the Ensembl and
1005 Ensembl Genomes REST API
1008 <!-- JAL-2049 -->Protein sequence variant annotation
1009 computed for 'sequence_variant' annotation on CDS regions
1013 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
1017 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
1018 Ref Fetcher fails to match, or otherwise updates sequence
1019 data from external database records.
1022 <!-- JAL-2154 -->Revised Jalview Project format for
1023 efficient recovery of sequence coding and alignment
1024 annotation relationships.
1026 </ul> <!-- <em>Applet</em>
1037 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
1041 <!-- JAL-2018-->Export features in Jalview format (again)
1042 includes graduated colourschemes
1045 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
1046 working with big alignments and lots of hidden columns
1049 <!-- JAL-2053-->Hidden column markers not always rendered
1050 at right of alignment window
1053 <!-- JAL-2067 -->Tidied up links in help file table of
1057 <!-- JAL-2072 -->Feature based tree calculation not shown
1061 <!-- JAL-2075 -->Hidden columns ignored during feature
1062 based tree calculation
1065 <!-- JAL-2065 -->Alignment view stops updating when show
1066 unconserved enabled for group on alignment
1069 <!-- JAL-2086 -->Cannot insert gaps into sequence when
1073 <!-- JAL-2146 -->Alignment column in status incorrectly
1074 shown as "Sequence position" when mousing over
1078 <!-- JAL-2099 -->Incorrect column numbers in ruler when
1079 hidden columns present
1082 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
1083 user created annotation added to alignment
1086 <!-- JAL-1841 -->RNA Structure consensus only computed for
1087 '()' base pair annotation
1090 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
1091 in zero scores for all base pairs in RNA Structure
1095 <!-- JAL-2174-->Extend selection with columns containing
1099 <!-- JAL-2275 -->Pfam format writer puts extra space at
1100 beginning of sequence
1103 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
1107 <!-- JAL-2238 -->Cannot create groups on an alignment from
1108 from a tree when t-coffee scores are shown
1111 <!-- JAL-1836,1967 -->Cannot import and view PDB
1112 structures with chains containing negative resnums (4q4h)
1115 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
1119 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
1120 to Clustal, PIR and PileUp output
1123 <!-- JAL-2008 -->Reordering sequence features that are
1124 not visible causes alignment window to repaint
1127 <!-- JAL-2006 -->Threshold sliders don't work in
1128 graduated colour and colour by annotation row for e-value
1129 scores associated with features and annotation rows
1132 <!-- JAL-1797 -->amino acid physicochemical conservation
1133 calculation should be case independent
1136 <!-- JAL-2173 -->Remove annotation also updates hidden
1140 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
1141 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
1142 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
1145 <!-- JAL-2065 -->Null pointer exceptions and redraw
1146 problems when reference sequence defined and 'show
1147 non-conserved' enabled
1150 <!-- JAL-1306 -->Quality and Conservation are now shown on
1151 load even when Consensus calculation is disabled
1154 <!-- JAL-1932 -->Remove right on penultimate column of
1155 alignment does nothing
1158 <em>Application</em>
1161 <!-- JAL-1552-->URLs and links can't be imported by
1162 drag'n'drop on OSX when launched via webstart (note - not
1163 yet fixed for El Capitan)
1166 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
1167 output when running on non-gb/us i18n platforms
1170 <!-- JAL-1944 -->Error thrown when exporting a view with
1171 hidden sequences as flat-file alignment
1174 <!-- JAL-2030-->InstallAnywhere distribution fails when
1178 <!-- JAL-2080-->Jalview very slow to launch via webstart
1179 (also hotfix for 2.9.0b2)
1182 <!-- JAL-2085 -->Cannot save project when view has a
1183 reference sequence defined
1186 <!-- JAL-1011 -->Columns are suddenly selected in other
1187 alignments and views when revealing hidden columns
1190 <!-- JAL-1989 -->Hide columns not mirrored in complement
1191 view in a cDNA/Protein splitframe
1194 <!-- JAL-1369 -->Cannot save/restore representative
1195 sequence from project when only one sequence is
1199 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
1200 in Structure Chooser
1203 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
1204 structure consensus didn't refresh annotation panel
1207 <!-- JAL-1962 -->View mapping in structure view shows
1208 mappings between sequence and all chains in a PDB file
1211 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
1212 dialogs format columns correctly, don't display array
1213 data, sort columns according to type
1216 <!-- JAL-1975 -->Export complete shown after destination
1217 file chooser is cancelled during an image export
1220 <!-- JAL-2025 -->Error when querying PDB Service with
1221 sequence name containing special characters
1224 <!-- JAL-2024 -->Manual PDB structure querying should be
1228 <!-- JAL-2104 -->Large tooltips with broken HTML
1229 formatting don't wrap
1232 <!-- JAL-1128 -->Figures exported from wrapped view are
1233 truncated so L looks like I in consensus annotation
1236 <!-- JAL-2003 -->Export features should only export the
1237 currently displayed features for the current selection or
1241 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
1242 after fetching cross-references, and restoring from
1246 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
1247 followed in the structure viewer
1250 <!-- JAL-2163 -->Titles for individual alignments in
1251 splitframe not restored from project
1254 <!-- JAL-2145 -->missing autocalculated annotation at
1255 trailing end of protein alignment in transcript/product
1256 splitview when pad-gaps not enabled by default
1259 <!-- JAL-1797 -->amino acid physicochemical conservation
1263 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
1264 article has been read (reopened issue due to
1265 internationalisation problems)
1268 <!-- JAL-1960 -->Only offer PDB structures in structure
1269 viewer based on sequence name, PDB and UniProt
1274 <!-- JAL-1976 -->No progress bar shown during export of
1278 <!-- JAL-2213 -->Structures not always superimposed after
1279 multiple structures are shown for one or more sequences.
1282 <!-- JAL-1370 -->Reference sequence characters should not
1283 be replaced with '.' when 'Show unconserved' format option
1287 <!-- JAL-1823 -->Cannot specify chain code when entering
1288 specific PDB id for sequence
1291 <!-- JAL-1944 -->File->Export->.. as doesn't work when
1292 'Export hidden sequences' is enabled, but 'export hidden
1293 columns' is disabled.
1296 <!--JAL-2026-->Best Quality option in structure chooser
1297 selects lowest rather than highest resolution structures
1301 <!-- JAL-1887 -->Incorrect start and end reported for PDB
1302 to sequence mapping in 'View Mappings' report
1305 <!-- JAL-2284 -->Unable to read old Jalview projects that
1306 contain non-XML data added after Jalvew wrote project.
1309 <!-- JAL-2118 -->Newly created annotation row reorders
1310 after clicking on it to create new annotation for a
1313 <!-- may exclude, this is an external service stability issue JAL-1941
1314 -- > RNA 3D structure not added via DSSR service</li> -->
1319 <!-- JAL-2151 -->Incorrect columns are selected when
1320 hidden columns present before start of sequence
1323 <!-- JAL-1986 -->Missing dependencies on applet pages
1327 <!-- JAL-1947 -->Overview pixel size changes when
1328 sequences are hidden in applet
1331 <!-- JAL-1996 -->Updated instructions for applet
1332 deployment on examples pages.
1339 <td width="60" nowrap>
1340 <div align="center">
1341 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
1342 <em>16/10/2015</em></strong>
1345 <td><em>General</em>
1347 <li>Time stamps for signed Jalview application and applet
1352 <em>Application</em>
1354 <li>Duplicate group consensus and conservation rows
1355 shown when tree is partitioned</li>
1356 <li>Erratic behaviour when tree partitions made with
1357 multiple cDNA/Protein split views</li>
1363 <td width="60" nowrap>
1364 <div align="center">
1365 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
1366 <em>8/10/2015</em></strong>
1369 <td><em>General</em>
1371 <li>Updated Spanish translations of localized text for
1373 </ul> <em>Application</em>
1375 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
1376 <li>Signed OSX InstallAnywhere installer<br></li>
1377 <li>Support for per-sequence based annotations in BioJSON</li>
1378 </ul> <em>Applet</em>
1380 <li>Split frame example added to applet examples page</li>
1381 </ul> <em>Build and Deployment</em>
1384 <!-- JAL-1888 -->New ant target for running Jalview's test
1392 <li>Mapping of cDNA to protein in split frames
1393 incorrect when sequence start > 1</li>
1394 <li>Broken images in filter column by annotation dialog
1396 <li>Feature colours not parsed from features file</li>
1397 <li>Exceptions and incomplete link URLs recovered when
1398 loading a features file containing HTML tags in feature
1402 <em>Application</em>
1404 <li>Annotations corrupted after BioJS export and
1406 <li>Incorrect sequence limits after Fetch DB References
1407 with 'trim retrieved sequences'</li>
1408 <li>Incorrect warning about deleting all data when
1409 deleting selected columns</li>
1410 <li>Patch to build system for shipping properly signed
1411 JNLP templates for webstart launch</li>
1412 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
1413 unreleased structures for download or viewing</li>
1414 <li>Tab/space/return keystroke operation of EMBL-PDBe
1415 fetcher/viewer dialogs works correctly</li>
1416 <li>Disabled 'minimise' button on Jalview windows
1417 running on OSX to workaround redraw hang bug</li>
1418 <li>Split cDNA/Protein view position and geometry not
1419 recovered from jalview project</li>
1420 <li>Initial enabled/disabled state of annotation menu
1421 sorter 'show autocalculated first/last' corresponds to
1423 <li>Restoring of Clustal, RNA Helices and T-Coffee
1424 color schemes from BioJSON</li>
1428 <li>Reorder sequences mirrored in cDNA/Protein split
1430 <li>Applet with Jmol examples not loading correctly</li>
1436 <td><div align="center">
1437 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
1439 <td><em>General</em>
1441 <li>Linked visualisation and analysis of DNA and Protein
1444 <li>Translated cDNA alignments shown as split protein
1445 and DNA alignment views</li>
1446 <li>Codon consensus annotation for linked protein and
1447 cDNA alignment views</li>
1448 <li>Link cDNA or Protein product sequences by loading
1449 them onto Protein or cDNA alignments</li>
1450 <li>Reconstruct linked cDNA alignment from aligned
1451 protein sequences</li>
1454 <li>Jmol integration updated to Jmol v14.2.14</li>
1455 <li>Import and export of Jalview alignment views as <a
1456 href="features/bioJsonFormat.html">BioJSON</a></li>
1457 <li>New alignment annotation file statements for
1458 reference sequences and marking hidden columns</li>
1459 <li>Reference sequence based alignment shading to
1460 highlight variation</li>
1461 <li>Select or hide columns according to alignment
1463 <li>Find option for locating sequences by description</li>
1464 <li>Conserved physicochemical properties shown in amino
1465 acid conservation row</li>
1466 <li>Alignments can be sorted by number of RNA helices</li>
1467 </ul> <em>Application</em>
1469 <li>New cDNA/Protein analysis capabilities
1471 <li>Get Cross-References should open a Split Frame
1472 view with cDNA/Protein</li>
1473 <li>Detect when nucleotide sequences and protein
1474 sequences are placed in the same alignment</li>
1475 <li>Split cDNA/Protein views are saved in Jalview
1480 <li>Use REST API to talk to Chimera</li>
1481 <li>Selected regions in Chimera are highlighted in linked
1482 Jalview windows</li>
1484 <li>VARNA RNA viewer updated to v3.93</li>
1485 <li>VARNA views are saved in Jalview Projects</li>
1486 <li>Pseudoknots displayed as Jalview RNA annotation can
1487 be shown in VARNA</li>
1489 <li>Make groups for selection uses marked columns as well
1490 as the active selected region</li>
1492 <li>Calculate UPGMA and NJ trees using sequence feature
1494 <li>New Export options
1496 <li>New Export Settings dialog to control hidden
1497 region export in flat file generation</li>
1499 <li>Export alignment views for display with the <a
1500 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
1502 <li>Export scrollable SVG in HTML page</li>
1503 <li>Optional embedding of BioJSON data when exporting
1504 alignment figures to HTML</li>
1506 <li>3D structure retrieval and display
1508 <li>Free text and structured queries with the PDBe
1510 <li>PDBe Search API based discovery and selection of
1511 PDB structures for a sequence set</li>
1515 <li>JPred4 employed for protein secondary structure
1517 <li>Hide Insertions menu option to hide unaligned columns
1518 for one or a group of sequences</li>
1519 <li>Automatically hide insertions in alignments imported
1520 from the JPred4 web server</li>
1521 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
1522 system on OSX<br />LGPL libraries courtesy of <a
1523 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
1525 <li>changed 'View nucleotide structure' submenu to 'View
1526 VARNA 2D Structure'</li>
1527 <li>change "View protein structure" menu option to "3D
1530 </ul> <em>Applet</em>
1532 <li>New layout for applet example pages</li>
1533 <li>New parameters to enable SplitFrame view
1534 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
1535 <li>New example demonstrating linked viewing of cDNA and
1536 Protein alignments</li>
1537 </ul> <em>Development and deployment</em>
1539 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
1540 <li>Include installation type and git revision in build
1541 properties and console log output</li>
1542 <li>Jalview Github organisation, and new github site for
1543 storing BioJsMSA Templates</li>
1544 <li>Jalview's unit tests now managed with TestNG</li>
1547 <!-- <em>General</em>
1549 </ul> --> <!-- issues resolved --> <em>Application</em>
1551 <li>Escape should close any open find dialogs</li>
1552 <li>Typo in select-by-features status report</li>
1553 <li>Consensus RNA secondary secondary structure
1554 predictions are not highlighted in amber</li>
1555 <li>Missing gap character in v2.7 example file means
1556 alignment appears unaligned when pad-gaps is not enabled</li>
1557 <li>First switch to RNA Helices colouring doesn't colour
1558 associated structure views</li>
1559 <li>ID width preference option is greyed out when auto
1560 width checkbox not enabled</li>
1561 <li>Stopped a warning dialog from being shown when
1562 creating user defined colours</li>
1563 <li>'View Mapping' in structure viewer shows sequence
1564 mappings for just that viewer's sequences</li>
1565 <li>Workaround for superposing PDB files containing
1566 multiple models in Chimera</li>
1567 <li>Report sequence position in status bar when hovering
1568 over Jmol structure</li>
1569 <li>Cannot output gaps as '.' symbols with Selection ->
1570 output to text box</li>
1571 <li>Flat file exports of alignments with hidden columns
1572 have incorrect sequence start/end</li>
1573 <li>'Aligning' a second chain to a Chimera structure from
1575 <li>Colour schemes applied to structure viewers don't
1576 work for nucleotide</li>
1577 <li>Loading/cut'n'pasting an empty or invalid file leads
1578 to a grey/invisible alignment window</li>
1579 <li>Exported Jpred annotation from a sequence region
1580 imports to different position</li>
1581 <li>Space at beginning of sequence feature tooltips shown
1582 on some platforms</li>
1583 <li>Chimera viewer 'View | Show Chain' menu is not
1585 <li>'New View' fails with a Null Pointer Exception in
1586 console if Chimera has been opened</li>
1587 <li>Mouseover to Chimera not working</li>
1588 <li>Miscellaneous ENA XML feature qualifiers not
1590 <li>NPE in annotation renderer after 'Extract Scores'</li>
1591 <li>If two structures in one Chimera window, mouseover of
1592 either sequence shows on first structure</li>
1593 <li>'Show annotations' options should not make
1594 non-positional annotations visible</li>
1595 <li>Subsequence secondary structure annotation not shown
1596 in right place after 'view flanking regions'</li>
1597 <li>File Save As type unset when current file format is
1599 <li>Save as '.jar' option removed for saving Jalview
1601 <li>Colour by Sequence colouring in Chimera more
1603 <li>Cannot 'add reference annotation' for a sequence in
1604 several views on same alignment</li>
1605 <li>Cannot show linked products for EMBL / ENA records</li>
1606 <li>Jalview's tooltip wraps long texts containing no
1608 </ul> <em>Applet</em>
1610 <li>Jmol to JalviewLite mouseover/link not working</li>
1611 <li>JalviewLite can't import sequences with ID
1612 descriptions containing angle brackets</li>
1613 </ul> <em>General</em>
1615 <li>Cannot export and reimport RNA secondary structure
1616 via jalview annotation file</li>
1617 <li>Random helix colour palette for colour by annotation
1618 with RNA secondary structure</li>
1619 <li>Mouseover to cDNA from STOP residue in protein
1620 translation doesn't work.</li>
1621 <li>hints when using the select by annotation dialog box</li>
1622 <li>Jmol alignment incorrect if PDB file has alternate CA
1624 <li>FontChooser message dialog appears to hang after
1625 choosing 1pt font</li>
1626 <li>Peptide secondary structure incorrectly imported from
1627 annotation file when annotation display text includes 'e' or
1629 <li>Cannot set colour of new feature type whilst creating
1631 <li>cDNA translation alignment should not be sequence
1632 order dependent</li>
1633 <li>'Show unconserved' doesn't work for lower case
1635 <li>Nucleotide ambiguity codes involving R not recognised</li>
1636 </ul> <em>Deployment and Documentation</em>
1638 <li>Applet example pages appear different to the rest of
1639 www.jalview.org</li>
1640 </ul> <em>Application Known issues</em>
1642 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
1643 <li>Misleading message appears after trying to delete
1645 <li>Jalview icon not shown in dock after InstallAnywhere
1646 version launches</li>
1647 <li>Fetching EMBL reference for an RNA sequence results
1648 fails with a sequence mismatch</li>
1649 <li>Corrupted or unreadable alignment display when
1650 scrolling alignment to right</li>
1651 <li>ArrayIndexOutOfBoundsException thrown when remove
1652 empty columns called on alignment with ragged gapped ends</li>
1653 <li>auto calculated alignment annotation rows do not get
1654 placed above or below non-autocalculated rows</li>
1655 <li>Jalview dekstop becomes sluggish at full screen in
1656 ultra-high resolution</li>
1657 <li>Cannot disable consensus calculation independently of
1658 quality and conservation</li>
1659 <li>Mouseover highlighting between cDNA and protein can
1660 become sluggish with more than one splitframe shown</li>
1661 </ul> <em>Applet Known Issues</em>
1663 <li>Core PDB parsing code requires Jmol</li>
1664 <li>Sequence canvas panel goes white when alignment
1665 window is being resized</li>
1671 <td><div align="center">
1672 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
1674 <td><em>General</em>
1676 <li>Updated Java code signing certificate donated by
1678 <li>Features and annotation preserved when performing
1679 pairwise alignment</li>
1680 <li>RNA pseudoknot annotation can be
1681 imported/exported/displayed</li>
1682 <li>'colour by annotation' can colour by RNA and
1683 protein secondary structure</li>
1684 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
1685 post-hoc with 2.9 release</em>)
1688 </ul> <em>Application</em>
1690 <li>Extract and display secondary structure for sequences
1691 with 3D structures</li>
1692 <li>Support for parsing RNAML</li>
1693 <li>Annotations menu for layout
1695 <li>sort sequence annotation rows by alignment</li>
1696 <li>place sequence annotation above/below alignment
1699 <li>Output in Stockholm format</li>
1700 <li>Internationalisation: improved Spanish (es)
1702 <li>Structure viewer preferences tab</li>
1703 <li>Disorder and Secondary Structure annotation tracks
1704 shared between alignments</li>
1705 <li>UCSF Chimera launch and linked highlighting from
1707 <li>Show/hide all sequence associated annotation rows for
1708 all or current selection</li>
1709 <li>disorder and secondary structure predictions
1710 available as dataset annotation</li>
1711 <li>Per-sequence rna helices colouring</li>
1714 <li>Sequence database accessions imported when fetching
1715 alignments from Rfam</li>
1716 <li>update VARNA version to 3.91</li>
1718 <li>New groovy scripts for exporting aligned positions,
1719 conservation values, and calculating sum of pairs scores.</li>
1720 <li>Command line argument to set default JABAWS server</li>
1721 <li>include installation type in build properties and
1722 console log output</li>
1723 <li>Updated Jalview project format to preserve dataset
1727 <!-- issues resolved --> <em>Application</em>
1729 <li>Distinguish alignment and sequence associated RNA
1730 structure in structure->view->VARNA</li>
1731 <li>Raise dialog box if user deletes all sequences in an
1733 <li>Pressing F1 results in documentation opening twice</li>
1734 <li>Sequence feature tooltip is wrapped</li>
1735 <li>Double click on sequence associated annotation
1736 selects only first column</li>
1737 <li>Redundancy removal doesn't result in unlinked
1738 leaves shown in tree</li>
1739 <li>Undos after several redundancy removals don't undo
1741 <li>Hide sequence doesn't hide associated annotation</li>
1742 <li>User defined colours dialog box too big to fit on
1743 screen and buttons not visible</li>
1744 <li>author list isn't updated if already written to
1745 Jalview properties</li>
1746 <li>Popup menu won't open after retrieving sequence
1748 <li>File open window for associate PDB doesn't open</li>
1749 <li>Left-then-right click on a sequence id opens a
1750 browser search window</li>
1751 <li>Cannot open sequence feature shading/sort popup menu
1752 in feature settings dialog</li>
1753 <li>better tooltip placement for some areas of Jalview
1755 <li>Allow addition of JABAWS Server which doesn't
1756 pass validation</li>
1757 <li>Web services parameters dialog box is too large to
1759 <li>Muscle nucleotide alignment preset obscured by
1761 <li>JABAWS preset submenus don't contain newly
1762 defined user preset</li>
1763 <li>MSA web services warns user if they were launched
1764 with invalid input</li>
1765 <li>Jalview cannot contact DAS Registy when running on
1768 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
1769 'Superpose with' submenu not shown when new view
1773 </ul> <!-- <em>Applet</em>
1775 </ul> <em>General</em>
1777 </ul>--> <em>Deployment and Documentation</em>
1779 <li>2G and 1G options in launchApp have no effect on
1780 memory allocation</li>
1781 <li>launchApp service doesn't automatically open
1782 www.jalview.org/examples/exampleFile.jar if no file is given</li>
1784 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
1785 InstallAnywhere reports cannot find valid JVM when Java
1786 1.7_055 is available
1788 </ul> <em>Application Known issues</em>
1791 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
1792 corrupted or unreadable alignment display when scrolling
1796 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
1797 retrieval fails but progress bar continues for DAS retrieval
1798 with large number of ID
1801 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
1802 flatfile output of visible region has incorrect sequence
1806 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
1807 rna structure consensus doesn't update when secondary
1808 structure tracks are rearranged
1811 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
1812 invalid rna structure positional highlighting does not
1813 highlight position of invalid base pairs
1816 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
1817 out of memory errors are not raised when saving Jalview
1818 project from alignment window file menu
1821 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
1822 Switching to RNA Helices colouring doesn't propagate to
1826 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
1827 colour by RNA Helices not enabled when user created
1828 annotation added to alignment
1831 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
1832 Jalview icon not shown on dock in Mountain Lion/Webstart
1834 </ul> <em>Applet Known Issues</em>
1837 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
1838 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
1841 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
1842 Jalview and Jmol example not compatible with IE9
1845 <li>Sort by annotation score doesn't reverse order
1851 <td><div align="center">
1852 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
1855 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
1858 <li>Internationalisation of user interface (usually
1859 called i18n support) and translation for Spanish locale</li>
1860 <li>Define/Undefine group on current selection with
1861 Ctrl-G/Shift Ctrl-G</li>
1862 <li>Improved group creation/removal options in
1863 alignment/sequence Popup menu</li>
1864 <li>Sensible precision for symbol distribution
1865 percentages shown in logo tooltip.</li>
1866 <li>Annotation panel height set according to amount of
1867 annotation when alignment first opened</li>
1868 </ul> <em>Application</em>
1870 <li>Interactive consensus RNA secondary structure
1871 prediction VIENNA RNAAliFold JABA 2.1 service</li>
1872 <li>Select columns containing particular features from
1873 Feature Settings dialog</li>
1874 <li>View all 'representative' PDB structures for selected
1876 <li>Update Jalview project format:
1878 <li>New file extension for Jalview projects '.jvp'</li>
1879 <li>Preserve sequence and annotation dataset (to
1880 store secondary structure annotation,etc)</li>
1881 <li>Per group and alignment annotation and RNA helix
1885 <li>New similarity measures for PCA and Tree calculation
1887 <li>Experimental support for retrieval and viewing of
1888 flanking regions for an alignment</li>
1892 <!-- issues resolved --> <em>Application</em>
1894 <li>logo keeps spinning and status remains at queued or
1895 running after job is cancelled</li>
1896 <li>cannot export features from alignments imported from
1897 Jalview/VAMSAS projects</li>
1898 <li>Buggy slider for web service parameters that take
1900 <li>Newly created RNA secondary structure line doesn't
1901 have 'display all symbols' flag set</li>
1902 <li>T-COFFEE alignment score shading scheme and other
1903 annotation shading not saved in Jalview project</li>
1904 <li>Local file cannot be loaded in freshly downloaded
1906 <li>Jalview icon not shown on dock in Mountain
1908 <li>Load file from desktop file browser fails</li>
1909 <li>Occasional NPE thrown when calculating large trees</li>
1910 <li>Cannot reorder or slide sequences after dragging an
1911 alignment onto desktop</li>
1912 <li>Colour by annotation dialog throws NPE after using
1913 'extract scores' function</li>
1914 <li>Loading/cut'n'pasting an empty file leads to a grey
1915 alignment window</li>
1916 <li>Disorder thresholds rendered incorrectly after
1917 performing IUPred disorder prediction</li>
1918 <li>Multiple group annotated consensus rows shown when
1919 changing 'normalise logo' display setting</li>
1920 <li>Find shows blank dialog after 'finished searching' if
1921 nothing matches query</li>
1922 <li>Null Pointer Exceptions raised when sorting by
1923 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
1925 <li>Errors in Jmol console when structures in alignment
1926 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
1928 <li>Not all working JABAWS services are shown in
1930 <li>JAVAWS version of Jalview fails to launch with
1931 'invalid literal/length code'</li>
1932 <li>Annotation/RNA Helix colourschemes cannot be applied
1933 to alignment with groups (actually fixed in 2.8.0b1)</li>
1934 <li>RNA Helices and T-Coffee Scores available as default
1937 </ul> <em>Applet</em>
1939 <li>Remove group option is shown even when selection is
1941 <li>Apply to all groups ticked but colourscheme changes
1942 don't affect groups</li>
1943 <li>Documented RNA Helices and T-Coffee Scores as valid
1944 colourscheme name</li>
1945 <li>Annotation labels drawn on sequence IDs when
1946 Annotation panel is not displayed</li>
1947 <li>Increased font size for dropdown menus on OSX and
1948 embedded windows</li>
1949 </ul> <em>Other</em>
1951 <li>Consensus sequence for alignments/groups with a
1952 single sequence were not calculated</li>
1953 <li>annotation files that contain only groups imported as
1954 annotation and junk sequences</li>
1955 <li>Fasta files with sequences containing '*' incorrectly
1956 recognised as PFAM or BLC</li>
1957 <li>conservation/PID slider apply all groups option
1958 doesn't affect background (2.8.0b1)
1960 <li>redundancy highlighting is erratic at 0% and 100%</li>
1961 <li>Remove gapped columns fails for sequences with ragged
1963 <li>AMSA annotation row with leading spaces is not
1964 registered correctly on import</li>
1965 <li>Jalview crashes when selecting PCA analysis for
1966 certain alignments</li>
1967 <li>Opening the colour by annotation dialog for an
1968 existing annotation based 'use original colours'
1969 colourscheme loses original colours setting</li>
1974 <td><div align="center">
1975 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
1976 <em>30/1/2014</em></strong>
1980 <li>Trusted certificates for JalviewLite applet and
1981 Jalview Desktop application<br />Certificate was donated by
1982 <a href="https://www.certum.eu">Certum</a> to the Jalview
1983 open source project).
1985 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
1986 <li>Output in Stockholm format</li>
1987 <li>Allow import of data from gzipped files</li>
1988 <li>Export/import group and sequence associated line
1989 graph thresholds</li>
1990 <li>Nucleotide substitution matrix that supports RNA and
1991 ambiguity codes</li>
1992 <li>Allow disorder predictions to be made on the current
1993 selection (or visible selection) in the same way that JPred
1995 <li>Groovy scripting for headless Jalview operation</li>
1996 </ul> <em>Other improvements</em>
1998 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
1999 <li>COMBINE statement uses current SEQUENCE_REF and
2000 GROUP_REF scope to group annotation rows</li>
2001 <li>Support '' style escaping of quotes in Newick
2003 <li>Group options for JABAWS service by command line name</li>
2004 <li>Empty tooltip shown for JABA service options with a
2005 link but no description</li>
2006 <li>Select primary source when selecting authority in
2007 database fetcher GUI</li>
2008 <li>Add .mfa to FASTA file extensions recognised by
2010 <li>Annotation label tooltip text wrap</li>
2015 <li>Slow scrolling when lots of annotation rows are
2017 <li>Lots of NPE (and slowness) after creating RNA
2018 secondary structure annotation line</li>
2019 <li>Sequence database accessions not imported when
2020 fetching alignments from Rfam</li>
2021 <li>Incorrect SHMR submission for sequences with
2023 <li>View all structures does not always superpose
2025 <li>Option widgets in service parameters not updated to
2026 reflect user or preset settings</li>
2027 <li>Null pointer exceptions for some services without
2028 presets or adjustable parameters</li>
2029 <li>Discover PDB IDs entry in structure menu doesn't
2030 discover PDB xRefs</li>
2031 <li>Exception encountered while trying to retrieve
2032 features with DAS</li>
2033 <li>Lowest value in annotation row isn't coloured
2034 when colour by annotation (per sequence) is coloured</li>
2035 <li>Keyboard mode P jumps to start of gapped region when
2036 residue follows a gap</li>
2037 <li>Jalview appears to hang importing an alignment with
2038 Wrap as default or after enabling Wrap</li>
2039 <li>'Right click to add annotations' message
2040 shown in wrap mode when no annotations present</li>
2041 <li>Disorder predictions fail with NPE if no automatic
2042 annotation already exists on alignment</li>
2043 <li>oninit javascript function should be called after
2044 initialisation completes</li>
2045 <li>Remove redundancy after disorder prediction corrupts
2046 alignment window display</li>
2047 <li>Example annotation file in documentation is invalid</li>
2048 <li>Grouped line graph annotation rows are not exported
2049 to annotation file</li>
2050 <li>Multi-harmony analysis cannot be run when only two
2052 <li>Cannot create multiple groups of line graphs with
2053 several 'combine' statements in annotation file</li>
2054 <li>Pressing return several times causes Number Format
2055 exceptions in keyboard mode</li>
2056 <li>Multi-harmony (SHMMR) method doesn't submit
2057 correct partitions for input data</li>
2058 <li>Translation from DNA to Amino Acids fails</li>
2059 <li>Jalview fail to load newick tree with quoted label</li>
2060 <li>--headless flag isn't understood</li>
2061 <li>ClassCastException when generating EPS in headless
2063 <li>Adjusting sequence-associated shading threshold only
2064 changes one row's threshold</li>
2065 <li>Preferences and Feature settings panel panel
2066 doesn't open</li>
2067 <li>hide consensus histogram also hides conservation and
2068 quality histograms</li>
2073 <td><div align="center">
2074 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
2076 <td><em>Application</em>
2078 <li>Support for JABAWS 2.0 Services (AACon alignment
2079 conservation, protein disorder and Clustal Omega)</li>
2080 <li>JABAWS server status indicator in Web Services
2082 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
2083 in Jalview alignment window</li>
2084 <li>Updated Jalview build and deploy framework for OSX
2085 mountain lion, windows 7, and 8</li>
2086 <li>Nucleotide substitution matrix for PCA that supports
2087 RNA and ambiguity codes</li>
2089 <li>Improved sequence database retrieval GUI</li>
2090 <li>Support fetching and database reference look up
2091 against multiple DAS sources (Fetch all from in 'fetch db
2093 <li>Jalview project improvements
2095 <li>Store and retrieve the 'belowAlignment'
2096 flag for annotation</li>
2097 <li>calcId attribute to group annotation rows on the
2099 <li>Store AACon calculation settings for a view in
2100 Jalview project</li>
2104 <li>horizontal scrolling gesture support</li>
2105 <li>Visual progress indicator when PCA calculation is
2107 <li>Simpler JABA web services menus</li>
2108 <li>visual indication that web service results are still
2109 being retrieved from server</li>
2110 <li>Serialise the dialogs that are shown when Jalview
2111 starts up for first time</li>
2112 <li>Jalview user agent string for interacting with HTTP
2114 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
2116 <li>Examples directory and Groovy library included in
2117 InstallAnywhere distribution</li>
2118 </ul> <em>Applet</em>
2120 <li>RNA alignment and secondary structure annotation
2121 visualization applet example</li>
2122 </ul> <em>General</em>
2124 <li>Normalise option for consensus sequence logo</li>
2125 <li>Reset button in PCA window to return dimensions to
2127 <li>Allow seqspace or Jalview variant of alignment PCA
2129 <li>PCA with either nucleic acid and protein substitution
2131 <li>Allow windows containing HTML reports to be exported
2133 <li>Interactive display and editing of RNA secondary
2134 structure contacts</li>
2135 <li>RNA Helix Alignment Colouring</li>
2136 <li>RNA base pair logo consensus</li>
2137 <li>Parse sequence associated secondary structure
2138 information in Stockholm files</li>
2139 <li>HTML Export database accessions and annotation
2140 information presented in tooltip for sequences</li>
2141 <li>Import secondary structure from LOCARNA clustalw
2142 style RNA alignment files</li>
2143 <li>import and visualise T-COFFEE quality scores for an
2145 <li>'colour by annotation' per sequence option to
2146 shade each sequence according to its associated alignment
2148 <li>New Jalview Logo</li>
2149 </ul> <em>Documentation and Development</em>
2151 <li>documentation for score matrices used in Jalview</li>
2152 <li>New Website!</li>
2154 <td><em>Application</em>
2156 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
2157 wsdbfetch REST service</li>
2158 <li>Stop windows being moved outside desktop on OSX</li>
2159 <li>Filetype associations not installed for webstart
2161 <li>Jalview does not always retrieve progress of a JABAWS
2162 job execution in full once it is complete</li>
2163 <li>revise SHMR RSBS definition to ensure alignment is
2164 uploaded via ali_file parameter</li>
2165 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
2166 <li>View all structures superposed fails with exception</li>
2167 <li>Jnet job queues forever if a very short sequence is
2168 submitted for prediction</li>
2169 <li>Cut and paste menu not opened when mouse clicked on
2171 <li>Putting fractional value into integer text box in
2172 alignment parameter dialog causes Jalview to hang</li>
2173 <li>Structure view highlighting doesn't work on
2175 <li>View all structures fails with exception shown in
2177 <li>Characters in filename associated with PDBEntry not
2178 escaped in a platform independent way</li>
2179 <li>Jalview desktop fails to launch with exception when
2181 <li>Tree calculation reports 'you must have 2 or more
2182 sequences selected' when selection is empty</li>
2183 <li>Jalview desktop fails to launch with jar signature
2184 failure when java web start temporary file caching is
2186 <li>DAS Sequence retrieval with range qualification
2187 results in sequence xref which includes range qualification</li>
2188 <li>Errors during processing of command line arguments
2189 cause progress bar (JAL-898) to be removed</li>
2190 <li>Replace comma for semi-colon option not disabled for
2191 DAS sources in sequence fetcher</li>
2192 <li>Cannot close news reader when JABAWS server warning
2193 dialog is shown</li>
2194 <li>Option widgets not updated to reflect user settings</li>
2195 <li>Edited sequence not submitted to web service</li>
2196 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
2197 <li>InstallAnywhere installer doesn't unpack and run
2198 on OSX Mountain Lion</li>
2199 <li>Annotation panel not given a scroll bar when
2200 sequences with alignment annotation are pasted into the
2202 <li>Sequence associated annotation rows not associated
2203 when loaded from Jalview project</li>
2204 <li>Browser launch fails with NPE on java 1.7</li>
2205 <li>JABAWS alignment marked as finished when job was
2206 cancelled or job failed due to invalid input</li>
2207 <li>NPE with v2.7 example when clicking on Tree
2208 associated with all views</li>
2209 <li>Exceptions when copy/paste sequences with grouped
2210 annotation rows to new window</li>
2211 </ul> <em>Applet</em>
2213 <li>Sequence features are momentarily displayed before
2214 they are hidden using hidefeaturegroups applet parameter</li>
2215 <li>loading features via javascript API automatically
2216 enables feature display</li>
2217 <li>scrollToColumnIn javascript API method doesn't
2219 </ul> <em>General</em>
2221 <li>Redundancy removal fails for rna alignment</li>
2222 <li>PCA calculation fails when sequence has been selected
2223 and then deselected</li>
2224 <li>PCA window shows grey box when first opened on OSX</li>
2225 <li>Letters coloured pink in sequence logo when alignment
2226 coloured with clustalx</li>
2227 <li>Choosing fonts without letter symbols defined causes
2228 exceptions and redraw errors</li>
2229 <li>Initial PCA plot view is not same as manually
2230 reconfigured view</li>
2231 <li>Grouped annotation graph label has incorrect line
2233 <li>Grouped annotation graph label display is corrupted
2234 for lots of labels</li>
2239 <div align="center">
2240 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
2243 <td><em>Application</em>
2245 <li>Jalview Desktop News Reader</li>
2246 <li>Tweaked default layout of web services menu</li>
2247 <li>View/alignment association menu to enable user to
2248 easily specify which alignment a multi-structure view takes
2249 its colours/correspondences from</li>
2250 <li>Allow properties file location to be specified as URL</li>
2251 <li>Extend Jalview project to preserve associations
2252 between many alignment views and a single Jmol display</li>
2253 <li>Store annotation row height in Jalview project file</li>
2254 <li>Annotation row column label formatting attributes
2255 stored in project file</li>
2256 <li>Annotation row order for auto-calculated annotation
2257 rows preserved in Jalview project file</li>
2258 <li>Visual progress indication when Jalview state is
2259 saved using Desktop window menu</li>
2260 <li>Visual indication that command line arguments are
2261 still being processed</li>
2262 <li>Groovy script execution from URL</li>
2263 <li>Colour by annotation default min and max colours in
2265 <li>Automatically associate PDB files dragged onto an
2266 alignment with sequences that have high similarity and
2268 <li>Update JGoogleAnalytics to latest release (0.3)</li>
2269 <li>'view structures' option to open many
2270 structures in same window</li>
2271 <li>Sort associated views menu option for tree panel</li>
2272 <li>Group all JABA and non-JABA services for a particular
2273 analysis function in its own submenu</li>
2274 </ul> <em>Applet</em>
2276 <li>Userdefined and autogenerated annotation rows for
2278 <li>Adjustment of alignment annotation pane height</li>
2279 <li>Annotation scrollbar for annotation panel</li>
2280 <li>Drag to reorder annotation rows in annotation panel</li>
2281 <li>'automaticScrolling' parameter</li>
2282 <li>Allow sequences with partial ID string matches to be
2283 annotated from GFF/Jalview features files</li>
2284 <li>Sequence logo annotation row in applet</li>
2285 <li>Absolute paths relative to host server in applet
2286 parameters are treated as such</li>
2287 <li>New in the JalviewLite javascript API:
2289 <li>JalviewLite.js javascript library</li>
2290 <li>Javascript callbacks for
2292 <li>Applet initialisation</li>
2293 <li>Sequence/alignment mouse-overs and selections</li>
2296 <li>scrollTo row and column alignment scrolling
2298 <li>Select sequence/alignment regions from javascript</li>
2299 <li>javascript structure viewer harness to pass
2300 messages between Jmol and Jalview when running as
2301 distinct applets</li>
2302 <li>sortBy method</li>
2303 <li>Set of applet and application examples shipped
2304 with documentation</li>
2305 <li>New example to demonstrate JalviewLite and Jmol
2306 javascript message exchange</li>
2308 </ul> <em>General</em>
2310 <li>Enable Jmol displays to be associated with multiple
2311 multiple alignments</li>
2312 <li>Option to automatically sort alignment with new tree</li>
2313 <li>User configurable link to enable redirects to a
2314 www.Jalview.org mirror</li>
2315 <li>Jmol colours option for Jmol displays</li>
2316 <li>Configurable newline string when writing alignment
2317 and other flat files</li>
2318 <li>Allow alignment annotation description lines to
2319 contain html tags</li>
2320 </ul> <em>Documentation and Development</em>
2322 <li>Add groovy test harness for bulk load testing to
2324 <li>Groovy script to load and align a set of sequences
2325 using a web service before displaying the result in the
2326 Jalview desktop</li>
2327 <li>Restructured javascript and applet api documentation</li>
2328 <li>Ant target to publish example html files with applet
2330 <li>Netbeans project for building Jalview from source</li>
2331 <li>ant task to create online javadoc for Jalview source</li>
2333 <td><em>Application</em>
2335 <li>User defined colourscheme throws exception when
2336 current built in colourscheme is saved as new scheme</li>
2337 <li>AlignFrame->Save in application pops up save
2338 dialog for valid filename/format</li>
2339 <li>Cannot view associated structure for UniProt sequence</li>
2340 <li>PDB file association breaks for UniProt sequence
2342 <li>Associate PDB from file dialog does not tell you
2343 which sequence is to be associated with the file</li>
2344 <li>Find All raises null pointer exception when query
2345 only matches sequence IDs</li>
2346 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
2347 <li>Jalview project with Jmol views created with Jalview
2348 2.4 cannot be loaded</li>
2349 <li>Filetype associations not installed for webstart
2351 <li>Two or more chains in a single PDB file associated
2352 with sequences in different alignments do not get coloured
2353 by their associated sequence</li>
2354 <li>Visibility status of autocalculated annotation row
2355 not preserved when project is loaded</li>
2356 <li>Annotation row height and visibility attributes not
2357 stored in Jalview project</li>
2358 <li>Tree bootstraps are not preserved when saved as a
2359 Jalview project</li>
2360 <li>Envision2 workflow tooltips are corrupted</li>
2361 <li>Enabling show group conservation also enables colour
2362 by conservation</li>
2363 <li>Duplicate group associated conservation or consensus
2364 created on new view</li>
2365 <li>Annotation scrollbar not displayed after 'show
2366 all hidden annotation rows' option selected</li>
2367 <li>Alignment quality not updated after alignment
2368 annotation row is hidden then shown</li>
2369 <li>Preserve colouring of structures coloured by
2370 sequences in pre Jalview 2.7 projects</li>
2371 <li>Web service job parameter dialog is not laid out
2373 <li>Web services menu not refreshed after 'reset
2374 services' button is pressed in preferences</li>
2375 <li>Annotation off by one in Jalview v2_3 example project</li>
2376 <li>Structures imported from file and saved in project
2377 get name like jalview_pdb1234.txt when reloaded</li>
2378 <li>Jalview does not always retrieve progress of a JABAWS
2379 job execution in full once it is complete</li>
2380 </ul> <em>Applet</em>
2382 <li>Alignment height set incorrectly when lots of
2383 annotation rows are displayed</li>
2384 <li>Relative URLs in feature HTML text not resolved to
2386 <li>View follows highlighting does not work for positions
2388 <li><= shown as = in tooltip</li>
2389 <li>Export features raises exception when no features
2391 <li>Separator string used for serialising lists of IDs
2392 for javascript api is modified when separator string
2393 provided as parameter</li>
2394 <li>Null pointer exception when selecting tree leaves for
2395 alignment with no existing selection</li>
2396 <li>Relative URLs for datasources assumed to be relative
2397 to applet's codebase</li>
2398 <li>Status bar not updated after finished searching and
2399 search wraps around to first result</li>
2400 <li>StructureSelectionManager instance shared between
2401 several Jalview applets causes race conditions and memory
2403 <li>Hover tooltip and mouseover of position on structure
2404 not sent from Jmol in applet</li>
2405 <li>Certain sequences of javascript method calls to
2406 applet API fatally hang browser</li>
2407 </ul> <em>General</em>
2409 <li>View follows structure mouseover scrolls beyond
2410 position with wrapped view and hidden regions</li>
2411 <li>Find sequence position moves to wrong residue
2412 with/without hidden columns</li>
2413 <li>Sequence length given in alignment properties window
2415 <li>InvalidNumberFormat exceptions thrown when trying to
2416 import PDB like structure files</li>
2417 <li>Positional search results are only highlighted
2418 between user-supplied sequence start/end bounds</li>
2419 <li>End attribute of sequence is not validated</li>
2420 <li>Find dialog only finds first sequence containing a
2421 given sequence position</li>
2422 <li>Sequence numbering not preserved in MSF alignment
2424 <li>Jalview PDB file reader does not extract sequence
2425 from nucleotide chains correctly</li>
2426 <li>Structure colours not updated when tree partition
2427 changed in alignment</li>
2428 <li>Sequence associated secondary structure not correctly
2429 parsed in interleaved stockholm</li>
2430 <li>Colour by annotation dialog does not restore current
2432 <li>Hiding (nearly) all sequences doesn't work
2434 <li>Sequences containing lowercase letters are not
2435 properly associated with their pdb files</li>
2436 </ul> <em>Documentation and Development</em>
2438 <li>schemas/JalviewWsParamSet.xsd corrupted by
2439 ApplyCopyright tool</li>
2444 <div align="center">
2445 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
2448 <td><em>Application</em>
2450 <li>New warning dialog when the Jalview Desktop cannot
2451 contact web services</li>
2452 <li>JABA service parameters for a preset are shown in
2453 service job window</li>
2454 <li>JABA Service menu entries reworded</li>
2458 <li>Modeller PIR IO broken - cannot correctly import a
2459 pir file emitted by Jalview</li>
2460 <li>Existing feature settings transferred to new
2461 alignment view created from cut'n'paste</li>
2462 <li>Improved test for mixed amino/nucleotide chains when
2463 parsing PDB files</li>
2464 <li>Consensus and conservation annotation rows
2465 occasionally become blank for all new windows</li>
2466 <li>Exception raised when right clicking above sequences
2467 in wrapped view mode</li>
2468 </ul> <em>Application</em>
2470 <li>multiple multiply aligned structure views cause cpu
2471 usage to hit 100% and computer to hang</li>
2472 <li>Web Service parameter layout breaks for long user
2473 parameter names</li>
2474 <li>Jaba service discovery hangs desktop if Jaba server
2481 <div align="center">
2482 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
2485 <td><em>Application</em>
2487 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
2488 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
2491 <li>Web Services preference tab</li>
2492 <li>Analysis parameters dialog box and user defined
2494 <li>Improved speed and layout of Envision2 service menu</li>
2495 <li>Superpose structures using associated sequence
2497 <li>Export coordinates and projection as CSV from PCA
2499 </ul> <em>Applet</em>
2501 <li>enable javascript: execution by the applet via the
2502 link out mechanism</li>
2503 </ul> <em>Other</em>
2505 <li>Updated the Jmol Jalview interface to work with Jmol
2507 <li>The Jalview Desktop and JalviewLite applet now
2508 require Java 1.5</li>
2509 <li>Allow Jalview feature colour specification for GFF
2510 sequence annotation files</li>
2511 <li>New 'colour by label' keword in Jalview feature file
2512 type colour specification</li>
2513 <li>New Jalview Desktop Groovy API method that allows a
2514 script to check if it being run in an interactive session or
2515 in a batch operation from the Jalview command line</li>
2519 <li>clustalx colourscheme colours Ds preferentially when
2520 both D+E are present in over 50% of the column</li>
2521 </ul> <em>Application</em>
2523 <li>typo in AlignmentFrame->View->Hide->all but
2524 selected Regions menu item</li>
2525 <li>sequence fetcher replaces ',' for ';' when the ',' is
2526 part of a valid accession ID</li>
2527 <li>fatal OOM if object retrieved by sequence fetcher
2528 runs out of memory</li>
2529 <li>unhandled Out of Memory Error when viewing pca
2530 analysis results</li>
2531 <li>InstallAnywhere builds fail to launch on OS X java
2532 10.5 update 4 (due to apple Java 1.6 update)</li>
2533 <li>Installanywhere Jalview silently fails to launch</li>
2534 </ul> <em>Applet</em>
2536 <li>Jalview.getFeatureGroups() raises an
2537 ArrayIndexOutOfBoundsException if no feature groups are
2544 <div align="center">
2545 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
2551 <li>Alignment prettyprinter doesn't cope with long
2553 <li>clustalx colourscheme colours Ds preferentially when
2554 both D+E are present in over 50% of the column</li>
2555 <li>nucleic acid structures retrieved from PDB do not
2556 import correctly</li>
2557 <li>More columns get selected than were clicked on when a
2558 number of columns are hidden</li>
2559 <li>annotation label popup menu not providing correct
2560 add/hide/show options when rows are hidden or none are
2562 <li>Stockholm format shown in list of readable formats,
2563 and parser copes better with alignments from RFAM.</li>
2564 <li>CSV output of consensus only includes the percentage
2565 of all symbols if sequence logo display is enabled</li>
2567 </ul> <em>Applet</em>
2569 <li>annotation panel disappears when annotation is
2571 </ul> <em>Application</em>
2573 <li>Alignment view not redrawn properly when new
2574 alignment opened where annotation panel is visible but no
2575 annotations are present on alignment</li>
2576 <li>pasted region containing hidden columns is
2577 incorrectly displayed in new alignment window</li>
2578 <li>Jalview slow to complete operations when stdout is
2579 flooded (fix is to close the Jalview console)</li>
2580 <li>typo in AlignmentFrame->View->Hide->all but
2581 selected Rregions menu item.</li>
2582 <li>inconsistent group submenu and Format submenu entry
2583 'Un' or 'Non'conserved</li>
2584 <li>Sequence feature settings are being shared by
2585 multiple distinct alignments</li>
2586 <li>group annotation not recreated when tree partition is
2588 <li>double click on group annotation to select sequences
2589 does not propagate to associated trees</li>
2590 <li>Mac OSX specific issues:
2592 <li>exception raised when mouse clicked on desktop
2593 window background</li>
2594 <li>Desktop menu placed on menu bar and application
2595 name set correctly</li>
2596 <li>sequence feature settings not wide enough for the
2597 save feature colourscheme button</li>
2606 <div align="center">
2607 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
2610 <td><em>New Capabilities</em>
2612 <li>URL links generated from description line for
2613 regular-expression based URL links (applet and application)
2615 <li>Non-positional feature URL links are shown in link
2617 <li>Linked viewing of nucleic acid sequences and
2619 <li>Automatic Scrolling option in View menu to display
2620 the currently highlighted region of an alignment.</li>
2621 <li>Order an alignment by sequence length, or using the
2622 average score or total feature count for each sequence.</li>
2623 <li>Shading features by score or associated description</li>
2624 <li>Subdivide alignment and groups based on identity of
2625 selected subsequence (Make Groups from Selection).</li>
2626 <li>New hide/show options including Shift+Control+H to
2627 hide everything but the currently selected region.</li>
2628 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
2629 </ul> <em>Application</em>
2631 <li>Fetch DB References capabilities and UI expanded to
2632 support retrieval from DAS sequence sources</li>
2633 <li>Local DAS Sequence sources can be added via the
2634 command line or via the Add local source dialog box.</li>
2635 <li>DAS Dbref and DbxRef feature types are parsed as
2636 database references and protein_name is parsed as
2637 description line (BioSapiens terms).</li>
2638 <li>Enable or disable non-positional feature and database
2639 references in sequence ID tooltip from View menu in
2641 <!-- <li>New hidden columns and rows and representatives capabilities
2642 in annotations file (in progress - not yet fully implemented)</li> -->
2643 <li>Group-associated consensus, sequence logos and
2644 conservation plots</li>
2645 <li>Symbol distributions for each column can be exported
2646 and visualized as sequence logos</li>
2647 <li>Optionally scale multi-character column labels to fit
2648 within each column of annotation row<!-- todo for applet -->
2650 <li>Optional automatic sort of associated alignment view
2651 when a new tree is opened.</li>
2652 <li>Jalview Java Console</li>
2653 <li>Better placement of desktop window when moving
2654 between different screens.</li>
2655 <li>New preference items for sequence ID tooltip and
2656 consensus annotation</li>
2657 <li>Client to submit sequences and IDs to Envision2
2659 <li><em>Vamsas Capabilities</em>
2661 <li>Improved VAMSAS synchronization (Jalview archive
2662 used to preserve views, structures, and tree display
2664 <li>Import of vamsas documents from disk or URL via
2666 <li>Sharing of selected regions between views and
2667 with other VAMSAS applications (Experimental feature!)</li>
2668 <li>Updated API to VAMSAS version 0.2</li>
2670 </ul> <em>Applet</em>
2672 <li>Middle button resizes annotation row height</li>
2675 <li>sortByTree (true/false) - automatically sort the
2676 associated alignment view by the tree when a new tree is
2678 <li>showTreeBootstraps (true/false) - show or hide
2679 branch bootstraps (default is to show them if available)</li>
2680 <li>showTreeDistances (true/false) - show or hide
2681 branch lengths (default is to show them if available)</li>
2682 <li>showUnlinkedTreeNodes (true/false) - indicate if
2683 unassociated nodes should be highlighted in the tree
2685 <li>heightScale and widthScale (1.0 or more) -
2686 increase the height or width of a cell in the alignment
2687 grid relative to the current font size.</li>
2690 <li>Non-positional features displayed in sequence ID
2692 </ul> <em>Other</em>
2694 <li>Features format: graduated colour definitions and
2695 specification of feature scores</li>
2696 <li>Alignment Annotations format: new keywords for group
2697 associated annotation (GROUP_REF) and annotation row display
2698 properties (ROW_PROPERTIES)</li>
2699 <li>XML formats extended to support graduated feature
2700 colourschemes, group associated annotation, and profile
2701 visualization settings.</li></td>
2704 <li>Source field in GFF files parsed as feature source
2705 rather than description</li>
2706 <li>Non-positional features are now included in sequence
2707 feature and gff files (controlled via non-positional feature
2708 visibility in tooltip).</li>
2709 <li>URL links generated for all feature links (bugfix)</li>
2710 <li>Added URL embedding instructions to features file
2712 <li>Codons containing ambiguous nucleotides translated as
2713 'X' in peptide product</li>
2714 <li>Match case switch in find dialog box works for both
2715 sequence ID and sequence string and query strings do not
2716 have to be in upper case to match case-insensitively.</li>
2717 <li>AMSA files only contain first column of
2718 multi-character column annotation labels</li>
2719 <li>Jalview Annotation File generation/parsing consistent
2720 with documentation (e.g. Stockholm annotation can be
2721 exported and re-imported)</li>
2722 <li>PDB files without embedded PDB IDs given a friendly
2724 <li>Find incrementally searches ID string matches as well
2725 as subsequence matches, and correctly reports total number
2729 <li>Better handling of exceptions during sequence
2731 <li>Dasobert generated non-positional feature URL
2732 link text excludes the start_end suffix</li>
2733 <li>DAS feature and source retrieval buttons disabled
2734 when fetch or registry operations in progress.</li>
2735 <li>PDB files retrieved from URLs are cached properly</li>
2736 <li>Sequence description lines properly shared via
2738 <li>Sequence fetcher fetches multiple records for all
2740 <li>Ensured that command line das feature retrieval
2741 completes before alignment figures are generated.</li>
2742 <li>Reduced time taken when opening file browser for
2744 <li>isAligned check prior to calculating tree, PCA or
2745 submitting an MSA to JNet now excludes hidden sequences.</li>
2746 <li>User defined group colours properly recovered
2747 from Jalview projects.</li>
2756 <div align="center">
2757 <strong>2.4.0.b2</strong><br> 28/10/2009
2762 <li>Experimental support for google analytics usage
2764 <li>Jalview privacy settings (user preferences and docs).</li>
2769 <li>Race condition in applet preventing startup in
2771 <li>Exception when feature created from selection beyond
2772 length of sequence.</li>
2773 <li>Allow synthetic PDB files to be imported gracefully</li>
2774 <li>Sequence associated annotation rows associate with
2775 all sequences with a given id</li>
2776 <li>Find function matches case-insensitively for sequence
2777 ID string searches</li>
2778 <li>Non-standard characters do not cause pairwise
2779 alignment to fail with exception</li>
2780 </ul> <em>Application Issues</em>
2782 <li>Sequences are now validated against EMBL database</li>
2783 <li>Sequence fetcher fetches multiple records for all
2785 </ul> <em>InstallAnywhere Issues</em>
2787 <li>Dock icon works for Mac OS X java (Mac 1.6 update
2788 issue with installAnywhere mechanism)</li>
2789 <li>Command line launching of JARs from InstallAnywhere
2790 version (java class versioning error fixed)</li>
2797 <div align="center">
2798 <strong>2.4</strong><br> 27/8/2008
2801 <td><em>User Interface</em>
2803 <li>Linked highlighting of codon and amino acid from
2804 translation and protein products</li>
2805 <li>Linked highlighting of structure associated with
2806 residue mapping to codon position</li>
2807 <li>Sequence Fetcher provides example accession numbers
2808 and 'clear' button</li>
2809 <li>MemoryMonitor added as an option under Desktop's
2811 <li>Extract score function to parse whitespace separated
2812 numeric data in description line</li>
2813 <li>Column labels in alignment annotation can be centred.</li>
2814 <li>Tooltip for sequence associated annotation give name
2816 </ul> <em>Web Services and URL fetching</em>
2818 <li>JPred3 web service</li>
2819 <li>Prototype sequence search client (no public services
2821 <li>Fetch either seed alignment or full alignment from
2823 <li>URL Links created for matching database cross
2824 references as well as sequence ID</li>
2825 <li>URL Links can be created using regular-expressions</li>
2826 </ul> <em>Sequence Database Connectivity</em>
2828 <li>Retrieval of cross-referenced sequences from other
2830 <li>Generalised database reference retrieval and
2831 validation to all fetchable databases</li>
2832 <li>Fetch sequences from DAS sources supporting the
2833 sequence command</li>
2834 </ul> <em>Import and Export</em>
2835 <li>export annotation rows as CSV for spreadsheet import</li>
2836 <li>Jalview projects record alignment dataset associations,
2837 EMBL products, and cDNA sequence mappings</li>
2838 <li>Sequence Group colour can be specified in Annotation
2840 <li>Ad-hoc colouring of group in Annotation File using RGB
2841 triplet as name of colourscheme</li>
2842 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
2844 <li>treenode binding for VAMSAS tree exchange</li>
2845 <li>local editing and update of sequences in VAMSAS
2846 alignments (experimental)</li>
2847 <li>Create new or select existing session to join</li>
2848 <li>load and save of vamsas documents</li>
2849 </ul> <em>Application command line</em>
2851 <li>-tree parameter to open trees (introduced for passing
2853 <li>-fetchfrom command line argument to specify nicknames
2854 of DAS servers to query for alignment features</li>
2855 <li>-dasserver command line argument to add new servers
2856 that are also automatically queried for features</li>
2857 <li>-groovy command line argument executes a given groovy
2858 script after all input data has been loaded and parsed</li>
2859 </ul> <em>Applet-Application data exchange</em>
2861 <li>Trees passed as applet parameters can be passed to
2862 application (when using "View in full
2863 application")</li>
2864 </ul> <em>Applet Parameters</em>
2866 <li>feature group display control parameter</li>
2867 <li>debug parameter</li>
2868 <li>showbutton parameter</li>
2869 </ul> <em>Applet API methods</em>
2871 <li>newView public method</li>
2872 <li>Window (current view) specific get/set public methods</li>
2873 <li>Feature display control methods</li>
2874 <li>get list of currently selected sequences</li>
2875 </ul> <em>New Jalview distribution features</em>
2877 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
2878 <li>RELEASE file gives build properties for the latest
2879 Jalview release.</li>
2880 <li>Java 1.1 Applet build made easier and donotobfuscate
2881 property controls execution of obfuscator</li>
2882 <li>Build target for generating source distribution</li>
2883 <li>Debug flag for javacc</li>
2884 <li>.jalview_properties file is documented (slightly) in
2885 jalview.bin.Cache</li>
2886 <li>Continuous Build Integration for stable and
2887 development version of Application, Applet and source
2892 <li>selected region output includes visible annotations
2893 (for certain formats)</li>
2894 <li>edit label/displaychar contains existing label/char
2896 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
2897 <li>shorter peptide product names from EMBL records</li>
2898 <li>Newick string generator makes compact representations</li>
2899 <li>bootstrap values parsed correctly for tree files with
2901 <li>pathological filechooser bug avoided by not allowing
2902 filenames containing a ':'</li>
2903 <li>Fixed exception when parsing GFF files containing
2904 global sequence features</li>
2905 <li>Alignment datasets are finalized only when number of
2906 references from alignment sequences goes to zero</li>
2907 <li>Close of tree branch colour box without colour
2908 selection causes cascading exceptions</li>
2909 <li>occasional negative imgwidth exceptions</li>
2910 <li>better reporting of non-fatal warnings to user when
2911 file parsing fails.</li>
2912 <li>Save works when Jalview project is default format</li>
2913 <li>Save as dialog opened if current alignment format is
2914 not a valid output format</li>
2915 <li>UniProt canonical names introduced for both das and
2917 <li>Histidine should be midblue (not pink!) in Zappo</li>
2918 <li>error messages passed up and output when data read
2920 <li>edit undo recovers previous dataset sequence when
2921 sequence is edited</li>
2922 <li>allow PDB files without pdb ID HEADER lines (like
2923 those generated by MODELLER) to be read in properly</li>
2924 <li>allow reading of JPred concise files as a normal
2926 <li>Stockholm annotation parsing and alignment properties
2927 import fixed for PFAM records</li>
2928 <li>Structure view windows have correct name in Desktop
2930 <li>annotation consisting of sequence associated scores
2931 can be read and written correctly to annotation file</li>
2932 <li>Aligned cDNA translation to aligned peptide works
2934 <li>Fixed display of hidden sequence markers and
2935 non-italic font for representatives in Applet</li>
2936 <li>Applet Menus are always embedded in applet window on
2938 <li>Newly shown features appear at top of stack (in
2940 <li>Annotations added via parameter not drawn properly
2941 due to null pointer exceptions</li>
2942 <li>Secondary structure lines are drawn starting from
2943 first column of alignment</li>
2944 <li>UniProt XML import updated for new schema release in
2946 <li>Sequence feature to sequence ID match for Features
2947 file is case-insensitive</li>
2948 <li>Sequence features read from Features file appended to
2949 all sequences with matching IDs</li>
2950 <li>PDB structure coloured correctly for associated views
2951 containing a sub-sequence</li>
2952 <li>PDB files can be retrieved by applet from Jar files</li>
2953 <li>feature and annotation file applet parameters
2954 referring to different directories are retrieved correctly</li>
2955 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
2956 <li>Fixed application hang whilst waiting for
2957 splash-screen version check to complete</li>
2958 <li>Applet properly URLencodes input parameter values
2959 when passing them to the launchApp service</li>
2960 <li>display name and local features preserved in results
2961 retrieved from web service</li>
2962 <li>Visual delay indication for sequence retrieval and
2963 sequence fetcher initialisation</li>
2964 <li>updated Application to use DAS 1.53e version of
2965 dasobert DAS client</li>
2966 <li>Re-instated Full AMSA support and .amsa file
2968 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
2976 <div align="center">
2977 <strong>2.3</strong><br> 9/5/07
2982 <li>Jmol 11.0.2 integration</li>
2983 <li>PDB views stored in Jalview XML files</li>
2984 <li>Slide sequences</li>
2985 <li>Edit sequence in place</li>
2986 <li>EMBL CDS features</li>
2987 <li>DAS Feature mapping</li>
2988 <li>Feature ordering</li>
2989 <li>Alignment Properties</li>
2990 <li>Annotation Scores</li>
2991 <li>Sort by scores</li>
2992 <li>Feature/annotation editing in applet</li>
2997 <li>Headless state operation in 2.2.1</li>
2998 <li>Incorrect and unstable DNA pairwise alignment</li>
2999 <li>Cut and paste of sequences with annotation</li>
3000 <li>Feature group display state in XML</li>
3001 <li>Feature ordering in XML</li>
3002 <li>blc file iteration selection using filename # suffix</li>
3003 <li>Stockholm alignment properties</li>
3004 <li>Stockhom alignment secondary structure annotation</li>
3005 <li>2.2.1 applet had no feature transparency</li>
3006 <li>Number pad keys can be used in cursor mode</li>
3007 <li>Structure Viewer mirror image resolved</li>
3014 <div align="center">
3015 <strong>2.2.1</strong><br> 12/2/07
3020 <li>Non standard characters can be read and displayed
3021 <li>Annotations/Features can be imported/exported to the
3023 <li>Applet allows editing of sequence/annotation/group
3024 name & description
3025 <li>Preference setting to display sequence name in
3027 <li>Annotation file format extended to allow
3028 Sequence_groups to be defined
3029 <li>Default opening of alignment overview panel can be
3030 specified in preferences
3031 <li>PDB residue numbering annotation added to associated
3037 <li>Applet crash under certain Linux OS with Java 1.6
3039 <li>Annotation file export / import bugs fixed
3040 <li>PNG / EPS image output bugs fixed
3046 <div align="center">
3047 <strong>2.2</strong><br> 27/11/06
3052 <li>Multiple views on alignment
3053 <li>Sequence feature editing
3054 <li>"Reload" alignment
3055 <li>"Save" to current filename
3056 <li>Background dependent text colour
3057 <li>Right align sequence ids
3058 <li>User-defined lower case residue colours
3061 <li>Menu item accelerator keys
3062 <li>Control-V pastes to current alignment
3063 <li>Cancel button for DAS Feature Fetching
3064 <li>PCA and PDB Viewers zoom via mouse roller
3065 <li>User-defined sub-tree colours and sub-tree selection
3067 <li>'New Window' button on the 'Output to Text box'
3072 <li>New memory efficient Undo/Redo System
3073 <li>Optimised symbol lookups and conservation/consensus
3075 <li>Region Conservation/Consensus recalculated after
3077 <li>Fixed Remove Empty Columns Bug (empty columns at end
3079 <li>Slowed DAS Feature Fetching for increased robustness.
3081 <li>Made angle brackets in ASCII feature descriptions
3083 <li>Re-instated Zoom function for PCA
3084 <li>Sequence descriptions conserved in web service
3086 <li>UniProt ID discoverer uses any word separated by
3088 <li>WsDbFetch query/result association resolved
3089 <li>Tree leaf to sequence mapping improved
3090 <li>Smooth fonts switch moved to FontChooser dialog box.
3097 <div align="center">
3098 <strong>2.1.1</strong><br> 12/9/06
3103 <li>Copy consensus sequence to clipboard</li>
3108 <li>Image output - rightmost residues are rendered if
3109 sequence id panel has been resized</li>
3110 <li>Image output - all offscreen group boundaries are
3112 <li>Annotation files with sequence references - all
3113 elements in file are relative to sequence position</li>
3114 <li>Mac Applet users can use Alt key for group editing</li>
3120 <div align="center">
3121 <strong>2.1</strong><br> 22/8/06
3126 <li>MAFFT Multiple Alignment in default Web Service list</li>
3127 <li>DAS Feature fetching</li>
3128 <li>Hide sequences and columns</li>
3129 <li>Export Annotations and Features</li>
3130 <li>GFF file reading / writing</li>
3131 <li>Associate structures with sequences from local PDB
3133 <li>Add sequences to exisiting alignment</li>
3134 <li>Recently opened files / URL lists</li>
3135 <li>Applet can launch the full application</li>
3136 <li>Applet has transparency for features (Java 1.2
3138 <li>Applet has user defined colours parameter</li>
3139 <li>Applet can load sequences from parameter
3140 "sequence<em>x</em>"
3146 <li>Redundancy Panel reinstalled in the Applet</li>
3147 <li>Monospaced font - EPS / rescaling bug fixed</li>
3148 <li>Annotation files with sequence references bug fixed</li>
3154 <div align="center">
3155 <strong>2.08.1</strong><br> 2/5/06
3160 <li>Change case of selected region from Popup menu</li>
3161 <li>Choose to match case when searching</li>
3162 <li>Middle mouse button and mouse movement can compress /
3163 expand the visible width and height of the alignment</li>
3168 <li>Annotation Panel displays complete JNet results</li>
3174 <div align="center">
3175 <strong>2.08b</strong><br> 18/4/06
3181 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
3182 <li>Righthand label on wrapped alignments shows correct
3189 <div align="center">
3190 <strong>2.08</strong><br> 10/4/06
3195 <li>Editing can be locked to the selection area</li>
3196 <li>Keyboard editing</li>
3197 <li>Create sequence features from searches</li>
3198 <li>Precalculated annotations can be loaded onto
3200 <li>Features file allows grouping of features</li>
3201 <li>Annotation Colouring scheme added</li>
3202 <li>Smooth fonts off by default - Faster rendering</li>
3203 <li>Choose to toggle Autocalculate Consensus On/Off</li>
3208 <li>Drag & Drop fixed on Linux</li>
3209 <li>Jalview Archive file faster to load/save, sequence
3210 descriptions saved.</li>
3216 <div align="center">
3217 <strong>2.07</strong><br> 12/12/05
3222 <li>PDB Structure Viewer enhanced</li>
3223 <li>Sequence Feature retrieval and display enhanced</li>
3224 <li>Choose to output sequence start-end after sequence
3225 name for file output</li>
3226 <li>Sequence Fetcher WSDBFetch@EBI</li>
3227 <li>Applet can read feature files, PDB files and can be
3228 used for HTML form input</li>
3233 <li>HTML output writes groups and features</li>
3234 <li>Group editing is Control and mouse click</li>
3235 <li>File IO bugs</li>
3241 <div align="center">
3242 <strong>2.06</strong><br> 28/9/05
3247 <li>View annotations in wrapped mode</li>
3248 <li>More options for PCA viewer</li>
3253 <li>GUI bugs resolved</li>
3254 <li>Runs with -nodisplay from command line</li>
3260 <div align="center">
3261 <strong>2.05b</strong><br> 15/9/05
3266 <li>Choose EPS export as lineart or text</li>
3267 <li>Jar files are executable</li>
3268 <li>Can read in Uracil - maps to unknown residue</li>
3273 <li>Known OutOfMemory errors give warning message</li>
3274 <li>Overview window calculated more efficiently</li>
3275 <li>Several GUI bugs resolved</li>
3281 <div align="center">
3282 <strong>2.05</strong><br> 30/8/05
3287 <li>Edit and annotate in "Wrapped" view</li>
3292 <li>Several GUI bugs resolved</li>
3298 <div align="center">
3299 <strong>2.04</strong><br> 24/8/05
3304 <li>Hold down mouse wheel & scroll to change font
3310 <li>Improved JPred client reliability</li>
3311 <li>Improved loading of Jalview files</li>
3317 <div align="center">
3318 <strong>2.03</strong><br> 18/8/05
3323 <li>Set Proxy server name and port in preferences</li>
3324 <li>Multiple URL links from sequence ids</li>
3325 <li>User Defined Colours can have a scheme name and added
3327 <li>Choose to ignore gaps in consensus calculation</li>
3328 <li>Unix users can set default web browser</li>
3329 <li>Runs without GUI for batch processing</li>
3330 <li>Dynamically generated Web Service Menus</li>
3335 <li>InstallAnywhere download for Sparc Solaris</li>
3341 <div align="center">
3342 <strong>2.02</strong><br> 18/7/05
3348 <li>Copy & Paste order of sequences maintains
3349 alignment order.</li>
3355 <div align="center">
3356 <strong>2.01</strong><br> 12/7/05
3361 <li>Use delete key for deleting selection.</li>
3362 <li>Use Mouse wheel to scroll sequences.</li>
3363 <li>Help file updated to describe how to add alignment
3365 <li>Version and build date written to build properties
3367 <li>InstallAnywhere installation will check for updates
3368 at launch of Jalview.</li>
3373 <li>Delete gaps bug fixed.</li>
3374 <li>FileChooser sorts columns.</li>
3375 <li>Can remove groups one by one.</li>
3376 <li>Filechooser icons installed.</li>
3377 <li>Finder ignores return character when searching.
3378 Return key will initiate a search.<br>
3385 <div align="center">
3386 <strong>2.0</strong><br> 20/6/05
3391 <li>New codebase</li>