4 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
5 * Copyright (C) $$Year-Rel$$ The Jalview Authors
7 * This file is part of Jalview.
9 * Jalview is free software: you can redistribute it and/or
10 * modify it under the terms of the GNU General Public License
11 * as published by the Free Software Foundation, either version 3
12 * of the License, or (at your option) any later version.
14 * Jalview is distributed in the hope that it will be useful, but
15 * WITHOUT ANY WARRANTY; without even the implied warranty
16 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
17 * PURPOSE. See the GNU General Public License for more details.
19 * You should have received a copy of the GNU General Public License
20 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
21 * The Jalview Authors are detailed in the 'AUTHORS' file.
24 <title>Release History</title>
27 /* remove bullets, narrower indent */
28 list-style-type: none;
35 /* separate the items from eachother */
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51 <strong>Release History</strong>
55 <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
56 <th><em>New Features</em></th>
57 <th><em>Issues Resolved</em></th>
60 <td width="60" align="center" nowrap><strong><a
61 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
66 <td align="left" valign="top"><em>Security</em>
69 <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate certificates.
75 <td width="60" align="center" nowrap><strong><a
76 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
77 <em>6/01/2022</em></strong></td>
79 <td align="left" valign="top"><em>Security</em>
82 <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
89 <td width="60" align="center" nowrap><strong><a
90 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
91 <em>20/12/2021</em></strong></td>
93 <td align="left" valign="top"><em>Security</em>
96 <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
98 </ul> <em>Development</em>
100 <li>Updated building instructions</li>
105 <!-- JAL-3840 -->Occupancy calculation is incorrect for
106 alignment columns with over -1+2^32 gaps (breaking filtering
110 <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
111 scale factors being set with buggy window-managers (linux
114 </ul> <em>Development</em>
116 <li>Fixed non-fatal gradle errors during build</li>
121 <td width="60" align="center" nowrap><strong><a
122 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
123 <em>09/03/2021</em></strong></td>
124 <td align="left" valign="top"><em>Improved control of
125 Jalview's use of network services via jalview_properties</em>
128 <!-- JAL-3814 -->New .jalview_properties token controlling
129 launch of the news browser (like -nonews argument)
132 <!-- JAL-3813 -->New .jalview_properties token controlling
133 download of linkout URLs from
134 www.jalview.org/services/identifiers
137 <!-- JAL-3812 -->New .jalview_properties token controlling
138 download of BIOJSHTML templates
141 <!-- JAL-3811 -->New 'Discover Web Services' option to
142 trigger a one off JABAWS discovery if autodiscovery was
146 <td align="left" valign="top">
149 <!-- JAL-3818 -->Intermittent deadlock opening structure in
152 </ul> <em>New Known defects</em>
155 <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
156 always restored from project (since 2.10.3)
159 <!-- JAL-3806 -->Selections from tree built from CDS aren't
160 propagated to Protein alignment (since 2.11.1.3)
166 <td width="60" align="center" nowrap><strong><a
167 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
168 <em>29/10/2020</em></strong></td>
169 <td align="left" valign="top">
174 <td align="left" valign="top">
177 <!-- JAL-3765 -->Find doesn't always highlight all matching
178 positions in a sequence (bug introduced in 2.11.1.2)
181 <!-- JAL-3760 -->Alignments containing one or more protein
182 sequences can be classed as nucleotide
185 <!-- JAL-3748 -->CDS alignment doesn't match original CDS
186 sequences after alignment of protein products (known defect
187 first reported for 2.11.1.0)
190 <!-- JAL-3725 -->No tooltip or popup menu for genomic
191 features outwith CDS shown overlaid on protein
194 <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
195 correctly mapped by Jalview (e.g. affects viral CDS with
196 ribosomal slippage, since 2.9.0)
199 <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
203 <!-- JAL-3700 -->Selections in CDS sequence panel don't
204 always select corresponding protein sequences
207 <!-- JAL-3759 --> <em>Make groups from selection</em> for a
208 column selection doesn't always ignore hidden columns
210 </ul> <em>Installer</em>
213 <!-- JAL-3611 -->Space character in Jalview install path on
214 Windows prevents install4j launching getdown
216 </ul> <em>Development</em>
219 <!-- JAL-3248 -->Fixed typos and specified compatible gradle
220 version numbers in doc/building.md
226 <td width="60" align="center" nowrap><strong><a
227 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
228 <em>25/09/2020</em></strong></td>
229 <td align="left" valign="top">
233 <td align="left" valign="top">
236 <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
237 "Encountered problems opening
238 https://www.jalview.org/examples/exampleFile_2_7.jvp"
244 <td width="60" align="center" nowrap><strong><a
245 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
246 <em>17/09/2020</em></strong></td>
247 <td align="left" valign="top">
250 <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
251 residue in cursor mode
254 <!-- JAL-3695 -->Support import of VCF 4.3 by updating
255 HTSJDK from 2.12 to 2.23
258 <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
259 optimisations and improvements suggested by Bob Hanson and
260 improved compatibility with JalviewJS
263 <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
264 alignments from Pfam and Rfam
267 <!-- JAL-2656 -->Recognise GZipped content for URLs and File
268 import (no longer based on .gz extension)
271 <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
274 <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
275 ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
279 <!-- JAL-3667 -->Improved warning messages, debug logging
280 and fixed Retry action when Jalview encounters errors when
281 saving or making backup files.
284 <!-- JAL-3676 -->Enhanced Jalview Java Console:
286 <li>Jalview's logging level can be configured</li>
287 <li>Copy to Clipboard Buttion</li>
291 <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
292 when running on Linux (Requires Java 11+)
294 </ul> <em>Launching Jalview</em>
297 <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
298 through a system property
301 <!-- JAL-3477 -->Improved built-in documentation and command
302 line help for configuring Jalview's memory
306 <td align="left" valign="top">
309 <!-- JAL-3691 -->Conservation and Quality tracks are shown
310 but not calculated and no protein or DNA score models are
311 available for tree/PCA calculation when launched with
312 Turkish language locale
315 <!-- JAL-3493 -->Escape does not clear highlights on the
316 alignment (Since Jalview 2.10.3)
319 <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
320 doesn't slide selected sequences, just sequence under cursor
323 <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
324 sequence under the cursor
327 <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
328 multiple EMBL gene products shown for a single contig
331 <!-- JAL-3696 -->Errors encountered when processing variants
332 from VCF files yield "Error processing VCF: Format specifier
336 <!-- JAL-3697 -->Count of features not shown can be wrong
337 when there are both local and complementary features mapped
338 to the position under the cursor
341 <!-- JAL-3673 -->Sequence ID for reference sequence is
342 clipped when Right align Sequence IDs enabled
345 <!-- JAL-2983 -->Slider with negative range values not
346 rendered correctly in VAqua4 (Since 2.10.4)
349 <!-- JAL-3685 -->Single quotes not displayed correctly in
350 internationalised text for some messages and log output
353 <!-- JAL-3490 -->Find doesn't report matches that span
354 hidden gapped columns
357 <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
358 panels, Alignment viewport and annotation renderer.
361 <!-- JAL-3561 -->Jalview ignores file format parameter
362 specifying output format when exporting an alignment via the
366 <!-- JAL-3667 -->Windows 10: For a minority of users, if
367 backups are not enabled, Jalview sometimes fails to
368 overwrite an existing file and raises a warning dialog. (in
369 2.11.0, and 2.11.1.0, the workaround is to try to save the
370 file again, and if that fails, delete the original file and
374 <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
378 <!-- JAL-3741 -->References to http://www.jalview.org in
379 program and documentation
381 </ul> <em>Launching Jalview</em>
384 <!-- JAL-3718 -->Jalview application fails when launched the
385 first time for a version that has different jars to the
386 previous launched version.
388 </ul> <em>Developing Jalview</em>
391 <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
392 data, causing cloverReport gradle task to fail with an
396 <!-- JAL-3280 -->Migrated the Jalview Version Checker to
397 monitor the release channel
399 </ul> <em>New Known defects</em>
402 <!-- JAL-3748 -->CDS shown in result of submitting proteins
403 in a CDS/Protein alignment to a web service is wrong when
404 proteins share a common transcript sequence (e.g.
405 genome of RNA viruses)
408 <!-- JAL-3576 -->Co-located features exported and re-imported
409 are ordered differently when shown on alignment and in
410 tooltips. (Also affects v2.11.1.0)
413 <!-- JAL-3702 -->Drag and drop of alignment file onto
414 alignment window when in a HiDPI scaled mode in Linux only
415 works for the top left quadrant of the alignment window
418 <!-- JAL-3701 -->Stale build data in jalview standalone jar
419 builds (only affects 2.11.1.1 branch)
422 <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
423 when alignment view restored from project (since Jalview 2.11.0)
426 <!-- JAL-3749 -->Duplicate CDS sequences are generated when
427 protein products for certain ENA records are repeatedly
428 shown via Calculate->Show Cross Refs
434 <td width="60" align="center" nowrap><strong><a
435 id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
436 <em>22/04/2020</em></strong></td>
437 <td align="left" valign="top">
440 <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
441 'virtual' codon features shown on protein (or vice versa)
442 for display in alignments, on structure views (including
443 transfer to UCSF chimera), in feature reports and for
447 <!-- JAL-3121 -->Feature attributes from VCF files can be
448 exported and re-imported as GFF3 files
451 <!-- JAL-3376 -->Capture VCF "fixed column" values
452 POS, ID, QUAL, FILTER as Feature Attributes
455 <!-- JAL-3375 -->More robust VCF numeric data field
456 validation while parsing
459 <!-- JAL-3533 -->Feature Settings dialog keeps same screen
463 <!-- JAL-3535 -->Feature Settings dialog title includes name
467 <!-- JAL-3538 -->Font anti-aliasing in alignment views
471 <!-- JAL-3468 -->Very long feature descriptions truncated in
475 <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
476 with no feature types visible
479 <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
481 </ul><em>Jalview Installer</em>
484 <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
485 in console (may be null when Jalview launched as executable jar or via conda)
488 <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
491 <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
494 <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
496 <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
497 </ul> <em>Release processes</em>
500 <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
503 <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
505 </ul> <em>Build System</em>
508 <!-- JAL-3510 -->Clover updated to 4.4.1
511 <!-- JAL-3513 -->Test code included in Clover coverage
515 <em>Groovy Scripts</em>
518 <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
519 to stdout containing the consensus sequence for each
520 alignment in a Jalview session
523 <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
524 genomic sequence_variant annotation from CDS as
525 missense_variant or synonymous_variant on protein products.
529 <td align="left" valign="top">
532 <!-- JAL-3581 -->Hidden sequence markers still visible when
533 'Show hidden markers' option is not ticked
536 <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
537 PNG output when 'Automatically set ID width' is set in
538 jalview preferences or properties file
541 <!-- JAL-3571 -->Feature Editor dialog can be opened when
542 'Show Sequence Features' option is not ticked
545 <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
546 buttons in Feature Settings dialog are clicked when no
550 <!-- JAL-3412 -->ID margins for CDS and Protein views not
551 equal when split frame is first opened
554 <!-- JAL-3296 -->Sequence position numbers in status bar not
555 correct after editing a sequence's start position
558 <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
559 with annotation and exceptions thrown when only a few
560 columns shown in wrapped mode
563 <!-- JAL-3386 -->Sequence IDs missing in headless export of
564 wrapped alignment figure with annotations
567 <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
568 ID fails with ClassCastException
571 <!-- JAL-3389 -->Chimera session not restored from Jalview
575 <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
576 feature settings dialog also selects columns
579 <!-- JAL-3473 -->SpinnerNumberModel causes
580 IllegalArgumentException in some circumstances
583 <!-- JAL-3534 -->Multiple feature settings dialogs can be
587 <!-- JAL-2764 -->Feature Settings dialog is orphaned if
588 alignment window is closed
591 <!-- JAL-3406 -->Credits missing some authors in Jalview
592 help documentation for 2.11.0 release
595 <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
596 includes Pfam ID as sequence's accession rather than its
599 </ul> <em>Java 11 Compatibility issues</em>
602 <!-- JAL-2987 -->OSX - Can't view some search results in
603 PDB/Uniprot search panel
605 </ul> <em>Installer</em>
608 <!-- JAL-3447 -->Jalview should not create file associations
609 for 3D structure files (.pdb, .mmcif. .cif)
611 </ul> <em>Repository and Source Release</em>
614 <!-- JAL-3474 -->removed obsolete .cvsignore files from
618 <!-- JAL-3541 -->Clover report generation running out of
621 </ul> <em>New Known Issues</em>
624 <!-- JAL-3523 -->OSX - Current working directory not
625 preserved when Jalview.app launched with parameters from
629 <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
630 clipped in headless figure export when Right Align option
634 <!-- JAL-3542 -->Jalview Installation type always reports
635 'Source' in console output
638 <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
639 bamboo server but run fine locally.
645 <td width="60" align="center" nowrap>
646 <strong><a name="Jalview.2.11.0">2.11.0</a><br />
647 <em>04/07/2019</em></strong>
649 <td align="left" valign="top">
652 <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
653 Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
654 source project) rather than InstallAnywhere
657 <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
658 settings, receive over the air updates and launch specific
659 versions via (<a href="https://github.com/threerings/getdown">Three
663 <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
664 formats supported by Jalview (including .jvp project files)
667 <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
668 arguments and switch between different getdown channels
671 <!-- JAL-3141 -->Backup files created when saving Jalview project
676 <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
677 <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
679 <!-- JAL-2620 -->Alternative genetic code tables for
680 'Translate as cDNA'</li>
682 <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
683 <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
686 <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
687 implementation that allows updates) used for Sequence Feature collections</li>
689 <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
690 features can be filtered and shaded according to any
691 associated attributes (e.g. variant attributes from VCF
692 file, or key-value pairs imported from column 9 of GFF
696 <!-- JAL-2879 -->Feature Attributes and shading schemes
697 stored and restored from Jalview Projects
700 <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
701 recognise variant features
704 <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
705 sequences (also coloured red by default)
708 <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
712 <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
713 algorithm (Z-sort/transparency and filter aware)
716 <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
722 <!-- JAL-3205 -->Symmetric score matrices for faster
723 tree and PCA calculations
725 <li><strong>Principal Components Analysis Viewer</strong>
728 <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
729 and Viewer state saved in Jalview Project
731 <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
734 <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
738 <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
743 <!-- JAL-3127 -->New 'Colour by Sequence ID' option
745 <li><strong>Speed and Efficiency</strong>
748 <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
749 multiple groups when working with large alignments
752 <!-- JAL-3200 -->Speedier import of annotation rows when parsing
756 <li><strong>User Interface</strong>
759 <!-- JAL-2933 -->Finder panel remembers last position in each
763 <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
764 what is shown)<br />Only visible regions of alignment are shown by
765 default (can be changed in user preferences)
768 <!-- JAL-3169 -->File Chooser stays open after responding Cancel
769 to the Overwrite Dialog
772 <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
776 <!-- JAL-1244 -->Status bar shows bounds when dragging a
777 selection region, and gap count when inserting or deleting gaps
780 <!-- JAL-3132 -->Status bar updates over sequence and annotation
784 <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
788 <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
792 <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
795 <!-- JAL-2621 -->Cursor changes over draggable box in Overview
799 <!-- JAL-3181 -->Consistent ordering of links in sequence id
803 <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
805 <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
809 <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
810 <li><strong>Java 11 Support (not yet on general release)</strong>
813 <!-- -->OSX GUI integrations for App menu's 'About' entry and
818 <em>Deprecations</em>
820 <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
821 capabilities removed from the Jalview Desktop
823 <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
824 unmarshalling has been replaced by JAXB for Jalview projects
825 and XML based data retrieval clients</li>
826 <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
827 <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
828 </ul> <em>Documentation</em>
830 <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
831 not supported in EPS figure export
833 <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
834 </ul> <em>Development and Release Processes</em>
837 <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
840 <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
842 <!-- JAL-3225 -->Eclipse project configuration managed with
846 <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
847 Bamboo continuous integration for unattended Test Suite
851 <!-- JAL-2864 -->Memory test suite to detect leaks in common
855 <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
859 <!-- JAL-3248 -->Developer documentation migrated to
860 markdown (with HTML rendering)
863 <!-- JAL-3287 -->HelpLinksChecker runs on Windows
866 <!-- JAL-3289 -->New URLs for publishing development
871 <td align="left" valign="top">
874 <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
877 <!-- JAL-3244 -->'View [Structure] Mappings' and structure
878 superposition in Jmol fail on Windows
881 <!-- JAL-3286 -->Blank error dialog is displayed when discovering
882 structures for sequences with lots of PDB structures
885 <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
889 <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
890 project involving multiple views
893 <!-- JAL-3164 -->Overview for complementary view in a linked
894 CDS/Protein alignment is not updated when Hide Columns by
895 Annotation dialog hides columns
898 <!-- JAL-3158 -->Selection highlighting in the complement of a
899 CDS/Protein alignment stops working after making a selection in
900 one view, then making another selection in the other view
903 <!-- JAL-3161 -->Annotations tooltip changes beyond visible
907 <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
908 Settings and Jalview Preferences panels
911 <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
912 overview with large alignments
915 <!-- JAL-2750 -->Tree and PCA calculation fails for selected
916 region if columns were selected by dragging right-to-left and the
917 mouse moved to the left of the first column
920 <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
921 hidden column marker via scale popup menu
924 <!-- JAL-2846 -->Error message for trying to load in invalid URLs
925 doesn't tell users the invalid URL
928 <!-- JAL-2816 -->Tooltips displayed for features filtered by
932 <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
933 show cross references or Fetch Database References are shown in
937 <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
938 peptide sequence (computed variant shown as p.Res.null)
941 <!-- JAL-2060 -->'Graduated colour' option not offered for
942 manually created features (where feature score is Float.NaN)
945 <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
946 when columns are hidden
949 <!-- JAL-3082 -->Regular expression error for '(' in Select
950 Columns by Annotation description
953 <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
954 out of Scale or Annotation Panel
957 <!-- JAL-3075 -->Column selection incorrect after scrolling out of
961 <!-- JAL-3074 -->Left/right drag in annotation can scroll
965 <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
969 <!-- JAL-3002 -->Column display is out by one after Page Down,
970 Page Up in wrapped mode
973 <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
976 <!-- JAL-2932 -->Finder searches in minimised alignments
979 <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
980 on opening an alignment
983 <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
987 <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
988 different groups in the alignment are selected
991 <!-- JAL-2717 -->Internationalised colour scheme names not shown
995 <!-- JAL-3206 -->Colour by Annotation can go black at min/max
999 <!-- JAL-3125 -->Value input for graduated feature colour
1000 threshold gets 'unrounded'
1003 <!-- JAL-2982 -->PCA image export doesn't respect background
1007 <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
1010 <!-- JAL-2959 -->PCA Print dialog continues after Cancel
1013 <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
1017 <!-- JAL-2964 -->Associate Tree with All Views not restored from
1021 <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
1022 shown in complementary view
1025 <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
1026 without normalisation
1029 <!-- JAL-3021 -->Sequence Details report should open positioned at top
1033 <!-- JAL-914 -->Help page can be opened twice
1036 <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
1038 </ul> <em>Editing</em>
1041 <!-- JAL-2822 -->Start and End should be updated when sequence
1042 data at beginning or end of alignment added/removed via 'Edit'
1046 <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
1047 relocate sequence features correctly when start of sequence is
1048 removed (Known defect since 2.10)
1051 <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
1052 dialog corrupts dataset sequence
1055 <!-- JAL-868 -->Structure colours not updated when associated tree
1056 repartitions the alignment view (Regression in 2.10.5)
1058 </ul> <em>Datamodel</em>
1061 <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
1062 sequence's End is greater than its length
1064 </ul> <em>Bugs fixed for Java 11 Support (not yet on
1065 general release)</em>
1068 <!-- JAL-3288 -->Menus work properly in split-screen
1070 </ul> <em>New Known Defects</em>
1073 <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
1076 <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
1077 regions of protein alignment.
1080 <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
1081 is restored from a Jalview 2.11 project
1084 <!-- JAL-3213 -->Alignment panel height can be too small after
1088 <!-- JAL-3240 -->Display is incorrect after removing gapped
1089 columns within hidden columns
1092 <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
1093 window after dragging left to select columns to left of visible
1097 <!-- JAL-2876 -->Features coloured according to their description
1098 string and thresholded by score in earlier versions of Jalview are
1099 not shown as thresholded features in 2.11. To workaround please
1100 create a Score filter instead.
1103 <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
1105 <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
1108 <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
1109 alignments with multiple views can close views unexpectedly
1112 <em>Java 11 Specific defects</em>
1115 <!-- JAL-3235 -->Jalview Properties file is not sorted
1116 alphabetically when saved
1122 <td width="60" nowrap>
1123 <div align="center">
1124 <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
1127 <td><div align="left">
1131 <!-- JAL-3101 -->Default memory for Jalview webstart and
1132 InstallAnywhere increased to 1G.
1135 <!-- JAL-247 -->Hidden sequence markers and representative
1136 sequence bolding included when exporting alignment as EPS,
1137 SVG, PNG or HTML. <em>Display is configured via the
1138 Format menu, or for command-line use via a Jalview
1139 properties file.</em>
1142 <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
1143 API and sequence data now imported as JSON.
1146 <!-- JAL-3065 -->Change in recommended way of starting
1147 Jalview via a Java command line: add jars in lib directory
1148 to CLASSPATH, rather than via the deprecated java.ext.dirs
1152 <em>Development</em>
1155 <!-- JAL-3047 -->Support added to execute test suite
1156 instrumented with <a href="http://openclover.org/">Open
1161 <td><div align="left">
1165 <!-- JAL-3104 -->Poorly scaled bar in quality annotation
1166 row shown in Feredoxin Structure alignment view of example
1170 <!-- JAL-2854 -->Annotation obscures sequences if lots of
1171 annotation displayed.
1174 <!-- JAL-3107 -->Group conservation/consensus not shown
1175 for newly created group when 'Apply to all groups'
1179 <!-- JAL-3087 -->Corrupted display when switching to
1180 wrapped mode when sequence panel's vertical scrollbar is
1184 <!-- JAL-3003 -->Alignment is black in exported EPS file
1185 when sequences are selected in exported view.</em>
1188 <!-- JAL-3059 -->Groups with different coloured borders
1189 aren't rendered with correct colour.
1192 <!-- JAL-3092 -->Jalview could hang when importing certain
1193 types of knotted RNA secondary structure.
1196 <!-- JAL-3095 -->Sequence highlight and selection in
1197 trimmed VARNA 2D structure is incorrect for sequences that
1201 <!-- JAL-3061 -->'.' inserted into RNA secondary structure
1202 annotation when columns are inserted into an alignment,
1203 and when exporting as Stockholm flatfile.
1206 <!-- JAL-3053 -->Jalview annotation rows containing upper
1207 and lower-case 'E' and 'H' do not automatically get
1208 treated as RNA secondary structure.
1211 <!-- JAL-3106 -->.jvp should be used as default extension
1212 (not .jar) when saving a Jalview project file.
1215 <!-- JAL-3105 -->Mac Users: closing a window correctly
1216 transfers focus to previous window on OSX
1219 <em>Java 10 Issues Resolved</em>
1222 <!-- JAL-2988 -->OSX - Can't save new files via the File
1223 or export menus by typing in a name into the Save dialog
1227 <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
1228 of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
1229 'look and feel' which has improved compatibility with the
1230 latest version of OSX.
1237 <td width="60" nowrap>
1238 <div align="center">
1239 <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
1240 <em>7/06/2018</em></strong>
1243 <td><div align="left">
1247 <!-- JAL-2920 -->Use HGVS nomenclature for variant
1248 annotation retrieved from Uniprot
1251 <!-- JAL-1460 -->Windows File Shortcuts can be dragged
1252 onto the Jalview Desktop
1256 <td><div align="left">
1260 <!-- JAL-3017 -->Cannot import features with multiple
1261 variant elements (blocks import of some Uniprot records)
1264 <!-- JAL-2997 -->Clustal files with sequence positions in
1265 right-hand column parsed correctly
1268 <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
1269 not alignment area in exported graphic
1272 <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
1273 window has input focus
1276 <!-- JAL-2992 -->Annotation panel set too high when
1277 annotation added to view (Windows)
1280 <!-- JAL-3009 -->Jalview Desktop is slow to start up when
1281 network connectivity is poor
1284 <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
1285 Jalview desktop on Windows doesn't open file<br /> <em>Dragging
1286 the currently open URL and links from a page viewed in
1287 Firefox or Chrome on Windows is now fully supported. If
1288 you are using Edge, only links in the page can be
1289 dragged, and with Internet Explorer, only the currently
1290 open URL in the browser can be dropped onto Jalview.</em>
1293 <em>New Known Defects</em>
1295 <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
1300 <td width="60" nowrap>
1301 <div align="center">
1302 <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
1305 <td><div align="left">
1309 <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
1310 for disabling automatic superposition of multiple
1311 structures and open structures in existing views
1314 <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
1315 ID and annotation area margins can be click-dragged to
1319 <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
1323 <!-- JAL-2759 -->Improved performance for large alignments
1324 and lots of hidden columns
1327 <!-- JAL-2593 -->Improved performance when rendering lots
1328 of features (particularly when transparency is disabled)
1331 <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
1332 exchange of Jalview features and Chimera attributes made
1338 <td><div align="left">
1341 <!-- JAL-2899 -->Structure and Overview aren't updated
1342 when Colour By Annotation threshold slider is adjusted
1345 <!-- JAL-2778 -->Slow redraw when Overview panel shown
1346 overlapping alignment panel
1349 <!-- JAL-2929 -->Overview doesn't show end of unpadded
1353 <!-- JAL-2789, JAL-2893 -->Cross-reference handling
1354 improved: CDS not handled correctly if transcript has no
1358 <!-- JAL-2321 -->Secondary structure and temperature
1359 factor annotation not added to sequence when local PDB
1360 file associated with it by drag'n'drop or structure
1364 <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
1365 dialog doesn't import PDB files dropped on an alignment
1368 <!-- JAL-2666 -->Linked scrolling via protein horizontal
1369 scroll bar doesn't work for some CDS/Protein views
1372 <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
1373 Java 1.8u153 onwards and Java 1.9u4+.
1376 <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
1377 columns in annotation row
1380 <!-- JAL-2913 -->Preferences panel's ID Width control is not
1381 honored in batch mode
1384 <!-- JAL-2945 -->Linked sequence highlighting doesn't work
1385 for structures added to existing Jmol view
1388 <!-- JAL-2223 -->'View Mappings' includes duplicate
1389 entries after importing project with multiple views
1392 <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
1393 protein sequences via SIFTS from associated PDB entries
1394 with negative residue numbers or missing residues fails
1397 <!-- JAL-2952 -->Exception when shading sequence with negative
1398 Temperature Factor values from annotated PDB files (e.g.
1399 as generated by CONSURF)
1402 <!-- JAL-2920 -->Uniprot 'sequence variant' features
1403 tooltip doesn't include a text description of mutation
1406 <!-- JAL-2922 -->Invert displayed features very slow when
1407 structure and/or overview windows are also shown
1410 <!-- JAL-2954 -->Selecting columns from highlighted regions
1411 very slow for alignments with large numbers of sequences
1414 <!-- JAL-2925 -->Copy Consensus fails for group consensus
1415 with 'StringIndexOutOfBounds'
1418 <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
1419 platforms running Java 10
1422 <!-- JAL-2960 -->Adding a structure to existing structure
1423 view appears to do nothing because the view is hidden behind the alignment view
1429 <!-- JAL-2926 -->Copy consensus sequence option in applet
1430 should copy the group consensus when popup is opened on it
1436 <!-- JAL-2913 -->Fixed ID width preference is not respected
1439 <em>New Known Defects</em>
1442 <!-- JAL-2973 --> Exceptions occasionally raised when
1443 editing a large alignment and overview is displayed
1446 <!-- JAL-2974 -->'Overview updating' progress bar is shown
1447 repeatedly after a series of edits even when the overview
1448 is no longer reflecting updates
1451 <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
1452 structures for protein subsequence (if 'Trim Retrieved
1453 Sequences' enabled) or Ensembl isoforms (Workaround in
1454 2.10.4 is to fail back to N&W mapping)
1457 <!-- JAL-2990 -->Export Annotations from File Menu with CSV
1458 option gives blank output
1465 <td width="60" nowrap>
1466 <div align="center">
1467 <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
1470 <td><div align="left">
1471 <ul><li>Updated Certum Codesigning Certificate
1472 (Valid till 30th November 2018)</li></ul></div></td>
1473 <td><div align="left">
1474 <em>Desktop</em><ul>
1476 <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
1477 <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
1478 <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
1479 <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
1480 <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
1481 <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
1482 <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
1488 <td width="60" nowrap>
1489 <div align="center">
1490 <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
1493 <td><div align="left">
1497 <!-- JAL-2446 -->Faster and more efficient management and
1498 rendering of sequence features
1501 <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
1502 429 rate limit request hander
1505 <!-- JAL-2773 -->Structure views don't get updated unless
1506 their colours have changed
1509 <!-- JAL-2495 -->All linked sequences are highlighted for
1510 a structure mousover (Jmol) or selection (Chimera)
1513 <!-- JAL-2790 -->'Cancel' button in progress bar for
1514 JABAWS AACon, RNAAliFold and Disorder prediction jobs
1517 <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
1518 view from Ensembl locus cross-references
1521 <!-- JAL-2685 -->Start/End limits are shown in Pairwise
1525 <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
1526 feature can be disabled
1529 <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
1530 PDB easier retrieval of sequences for lists of IDs
1533 <!-- JAL-2758 -->Short names for sequences retrieved from
1539 <li>Groovy interpreter updated to 2.4.12</li>
1540 <li>Example groovy script for generating a matrix of
1541 percent identity scores for current alignment.</li>
1543 <em>Testing and Deployment</em>
1546 <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
1550 <td><div align="left">
1554 <!-- JAL-2643 -->Pressing tab after updating the colour
1555 threshold text field doesn't trigger an update to the
1559 <!-- JAL-2682 -->Race condition when parsing sequence ID
1563 <!-- JAL-2608 -->Overview windows are also closed when
1564 alignment window is closed
1567 <!-- JAL-2548 -->Export of features doesn't always respect
1571 <!-- JAL-2831 -->Jumping from column 1 to column 100,000
1572 takes a long time in Cursor mode
1578 <!-- JAL-2777 -->Structures with whitespace chainCode
1579 cannot be viewed in Chimera
1582 <!-- JAL-2728 -->Protein annotation panel too high in
1586 <!-- JAL-2757 -->Can't edit the query after the server
1587 error warning icon is shown in Uniprot and PDB Free Text
1591 <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
1594 <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
1597 <!-- JAL-2739 -->Hidden column marker in last column not
1598 rendered when switching back from Wrapped to normal view
1601 <!-- JAL-2768 -->Annotation display corrupted when
1602 scrolling right in unwapped alignment view
1605 <!-- JAL-2542 -->Existing features on subsequence
1606 incorrectly relocated when full sequence retrieved from
1610 <!-- JAL-2733 -->Last reported memory still shown when
1611 Desktop->Show Memory is unticked (OSX only)
1614 <!-- JAL-2658 -->Amend Features dialog doesn't allow
1615 features of same type and group to be selected for
1619 <!-- JAL-2524 -->Jalview becomes sluggish in wide
1620 alignments when hidden columns are present
1623 <!-- JAL-2392 -->Jalview freezes when loading and
1624 displaying several structures
1627 <!-- JAL-2732 -->Black outlines left after resizing or
1631 <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
1632 within the Jalview desktop on OSX
1635 <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
1636 when in wrapped alignment mode
1639 <!-- JAL-2636 -->Scale mark not shown when close to right
1640 hand end of alignment
1643 <!-- JAL-2684 -->Pairwise alignment of selected regions of
1644 each selected sequence do not have correct start/end
1648 <!-- JAL-2793 -->Alignment ruler height set incorrectly
1649 after canceling the Alignment Window's Font dialog
1652 <!-- JAL-2036 -->Show cross-references not enabled after
1653 restoring project until a new view is created
1656 <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
1657 URL links appears when only default EMBL-EBI link is
1658 configured (since 2.10.2b2)
1661 <!-- JAL-2775 -->Overview redraws whole window when box
1662 position is adjusted
1665 <!-- JAL-2225 -->Structure viewer doesn't map all chains
1666 in a multi-chain structure when viewing alignment
1667 involving more than one chain (since 2.10)
1670 <!-- JAL-2811 -->Double residue highlights in cursor mode
1671 if new selection moves alignment window
1674 <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
1675 arrow key in cursor mode to pass hidden column marker
1678 <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
1679 that produces correctly annotated transcripts and products
1682 <!-- JAL-2776 -->Toggling a feature group after first time
1683 doesn't update associated structure view
1686 <em>Applet</em><br />
1689 <!-- JAL-2687 -->Concurrent modification exception when
1690 closing alignment panel
1693 <em>BioJSON</em><br />
1696 <!-- JAL-2546 -->BioJSON export does not preserve
1697 non-positional features
1700 <em>New Known Issues</em>
1703 <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
1704 sequence features correctly (for many previous versions of
1708 <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
1709 using cursor in wrapped panel other than top
1712 <!-- JAL-2791 -->Select columns containing feature ignores
1713 graduated colour threshold
1716 <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
1717 always preserve numbering and sequence features
1720 <em>Known Java 9 Issues</em>
1723 <!-- JAL-2902 -->Groovy Console very slow to open and is
1724 not responsive when entering characters (Webstart, Java
1731 <td width="60" nowrap>
1732 <div align="center">
1733 <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
1734 <em>2/10/2017</em></strong>
1737 <td><div align="left">
1738 <em>New features in Jalview Desktop</em>
1741 <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
1743 <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
1747 <td><div align="left">
1751 <td width="60" nowrap>
1752 <div align="center">
1753 <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
1754 <em>7/9/2017</em></strong>
1757 <td><div align="left">
1761 <!-- JAL-2588 -->Show gaps in overview window by colouring
1762 in grey (sequences used to be coloured grey, and gaps were
1766 <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
1770 <!-- JAL-2587 -->Overview updates immediately on increase
1771 in size and progress bar shown as higher resolution
1772 overview is recalculated
1777 <td><div align="left">
1781 <!-- JAL-2664 -->Overview window redraws every hidden
1782 column region row by row
1785 <!-- JAL-2681 -->duplicate protein sequences shown after
1786 retrieving Ensembl crossrefs for sequences from Uniprot
1789 <!-- JAL-2603 -->Overview window throws NPE if show boxes
1790 format setting is unticked
1793 <!-- JAL-2610 -->Groups are coloured wrongly in overview
1794 if group has show boxes format setting unticked
1797 <!-- JAL-2672,JAL-2665 -->Redraw problems when
1798 autoscrolling whilst dragging current selection group to
1799 include sequences and columns not currently displayed
1802 <!-- JAL-2691 -->Not all chains are mapped when multimeric
1803 assemblies are imported via CIF file
1806 <!-- JAL-2704 -->Gap colour in custom colourscheme is not
1807 displayed when threshold or conservation colouring is also
1811 <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
1815 <!-- JAL-2673 -->Jalview continues to scroll after
1816 dragging a selected region off the visible region of the
1820 <!-- JAL-2724 -->Cannot apply annotation based
1821 colourscheme to all groups in a view
1824 <!-- JAL-2511 -->IDs don't line up with sequences
1825 initially after font size change using the Font chooser or
1832 <td width="60" nowrap>
1833 <div align="center">
1834 <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
1837 <td><div align="left">
1838 <em>Calculations</em>
1842 <!-- JAL-1933 -->Occupancy annotation row shows number of
1843 ungapped positions in each column of the alignment.
1846 <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
1847 a calculation dialog box
1850 <!-- JAL-2379 -->Revised implementation of PCA for speed
1851 and memory efficiency (~30x faster)
1854 <!-- JAL-2403 -->Revised implementation of sequence
1855 similarity scores as used by Tree, PCA, Shading Consensus
1856 and other calculations
1859 <!-- JAL-2416 -->Score matrices are stored as resource
1860 files within the Jalview codebase
1863 <!-- JAL-2500 -->Trees computed on Sequence Feature
1864 Similarity may have different topology due to increased
1871 <!-- JAL-2360,JAL-2371, -->More robust colours and shader
1872 model for alignments and groups
1875 <!-- JAL-384 -->Custom shading schemes created via groovy
1882 <!-- JAL-2526 -->Efficiency improvements for interacting
1883 with alignment and overview windows
1886 <!-- JAL-2514 -->Scrolling of wrapped alignment views via
1890 <!-- JAL-2388 -->Hidden columns and sequences can be
1894 <!-- JAL-2611 -->Click-drag in visible area allows fine
1895 adjustment of visible position
1899 <em>Data import/export</em>
1902 <!-- JAL-2535 -->Posterior probability annotation from
1903 Stockholm files imported as sequence associated annotation
1906 <!-- JAL-2507 -->More robust per-sequence positional
1907 annotation input/output via stockholm flatfile
1910 <!-- JAL-2533 -->Sequence names don't include file
1911 extension when importing structure files without embedded
1912 names or PDB accessions
1915 <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
1916 format sequence substitution matrices
1919 <em>User Interface</em>
1922 <!-- JAL-2447 --> Experimental Features Checkbox in
1923 Desktop's Tools menu to hide or show untested features in
1927 <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
1928 via Overview or sequence motif search operations
1931 <!-- JAL-2547 -->Amend sequence features dialog box can be
1932 opened by double clicking gaps within sequence feature
1936 <!-- JAL-1476 -->Status bar message shown when not enough
1937 aligned positions were available to create a 3D structure
1941 <em>3D Structure</em>
1944 <!-- JAL-2430 -->Hidden regions in alignment views are not
1945 coloured in linked structure views
1948 <!-- JAL-1596 -->Faster Chimera/Jalview communication by
1949 file-based command exchange
1952 <!-- JAL-2375 -->Structure chooser automatically shows
1953 Cached Structures rather than querying the PDBe if
1954 structures are already available for sequences
1957 <!-- JAL-2520 -->Structures imported via URL are cached in
1958 the Jalview project rather than downloaded again when the
1959 project is reopened.
1962 <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
1963 to transfer Chimera's structure attributes as Jalview
1964 features, and vice-versa (<strong>Experimental
1968 <em>Web Services</em>
1971 <!-- JAL-2549 -->Updated JABAWS client to v2.2
1974 <!-- JAL-2335 -->Filter non-standard amino acids and
1975 nucleotides when submitting to AACon and other MSA
1979 <!-- JAL-2316, -->URLs for viewing database
1980 cross-references provided by identifiers.org and the
1981 EMBL-EBI's MIRIAM DB
1988 <!-- JAL-2344 -->FileFormatI interface for describing and
1989 identifying file formats (instead of String constants)
1992 <!-- JAL-2228 -->FeatureCounter script refactored for
1993 efficiency when counting all displayed features (not
1994 backwards compatible with 2.10.1)
1997 <em>Example files</em>
2000 <!-- JAL-2631 -->Graduated feature colour style example
2001 included in the example feature file
2004 <em>Documentation</em>
2007 <!-- JAL-2339 -->Release notes reformatted for readability
2008 with the built-in Java help viewer
2011 <!-- JAL-1644 -->Find documentation updated with 'search
2012 sequence description' option
2018 <!-- JAL-2485, -->External service integration tests for
2019 Uniprot REST Free Text Search Client
2022 <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
2025 <!-- JAL-2326 -->Prevent or clear modal dialogs raised
2030 <td><div align="left">
2031 <em>Calculations</em>
2034 <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
2035 matrix - C->R should be '-3'<br />Old matrix restored
2036 with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
2038 <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
2039 Jalview's treatment of gaps in PCA and substitution matrix
2040 based Tree calculations.<br /> <br />In earlier versions
2041 of Jalview, gaps matching gaps were penalised, and gaps
2042 matching non-gaps penalised even more. In the PCA
2043 calculation, gaps were actually treated as non-gaps - so
2044 different costs were applied, which meant Jalview's PCAs
2045 were different to those produced by SeqSpace.<br />Jalview
2046 now treats gaps in the same way as SeqSpace (ie it scores
2047 them as 0). <br /> <br />Enter the following in the
2048 Groovy console to restore pre-2.10.2 behaviour:<br />
2049 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
2050 // for 2.10.1 mode <br />
2051 jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
2052 // to restore 2.10.2 mode <br /> <br /> <em>Note:
2053 these settings will affect all subsequent tree and PCA
2054 calculations (not recommended)</em></li>
2056 <!-- JAL-2424 -->Fixed off-by-one bug that affected
2057 scaling of branch lengths for trees computed using
2058 Sequence Feature Similarity.
2061 <!-- JAL-2377 -->PCA calculation could hang when
2062 generating output report when working with highly
2063 redundant alignments
2066 <!-- JAL-2544 --> Sort by features includes features to
2067 right of selected region when gaps present on right-hand
2071 <em>User Interface</em>
2074 <!-- JAL-2346 -->Reopening Colour by annotation dialog
2075 doesn't reselect a specific sequence's associated
2076 annotation after it was used for colouring a view
2079 <!-- JAL-2419 -->Current selection lost if popup menu
2080 opened on a region of alignment without groups
2083 <!-- JAL-2374 -->Popup menu not always shown for regions
2084 of an alignment with overlapping groups
2087 <!-- JAL-2310 -->Finder double counts if both a sequence's
2088 name and description match
2091 <!-- JAL-2370 -->Hiding column selection containing two
2092 hidden regions results in incorrect hidden regions
2095 <!-- JAL-2386 -->'Apply to all groups' setting when
2096 changing colour does not apply Conservation slider value
2100 <!-- JAL-2373 -->Percentage identity and conservation menu
2101 items do not show a tick or allow shading to be disabled
2104 <!-- JAL-2385 -->Conservation shading or PID threshold
2105 lost when base colourscheme changed if slider not visible
2108 <!-- JAL-2547 -->Sequence features shown in tooltip for
2109 gaps before start of features
2112 <!-- JAL-2623 -->Graduated feature colour threshold not
2113 restored to UI when feature colour is edited
2116 <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
2117 a time when scrolling vertically in wrapped mode.
2120 <!-- JAL-2630 -->Structure and alignment overview update
2121 as graduate feature colour settings are modified via the
2125 <!-- JAL-2034 -->Overview window doesn't always update
2126 when a group defined on the alignment is resized
2129 <!-- JAL-2605 -->Mouseovers on left/right scale region in
2130 wrapped view result in positional status updates
2134 <!-- JAL-2563 -->Status bar doesn't show position for
2135 ambiguous amino acid and nucleotide symbols
2138 <!-- JAL-2602 -->Copy consensus sequence failed if
2139 alignment included gapped columns
2142 <!-- JAL-2473 -->Minimum size set for Jalview windows so
2143 widgets don't permanently disappear
2146 <!-- JAL-2503 -->Cannot select or filter quantitative
2147 annotation that are shown only as column labels (e.g.
2148 T-Coffee column reliability scores)
2151 <!-- JAL-2594 -->Exception thrown if trying to create a
2152 sequence feature on gaps only
2155 <!-- JAL-2504 -->Features created with 'New feature'
2156 button from a Find inherit previously defined feature type
2157 rather than the Find query string
2160 <!-- JAL-2423 -->incorrect title in output window when
2161 exporting tree calculated in Jalview
2164 <!-- JAL-2437 -->Hiding sequences at bottom of alignment
2165 and then revealing them reorders sequences on the
2169 <!-- JAL-964 -->Group panel in sequence feature settings
2170 doesn't update to reflect available set of groups after
2171 interactively adding or modifying features
2174 <!-- JAL-2225 -->Sequence Database chooser unusable on
2178 <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
2179 only excluded gaps in current sequence and ignored
2186 <!-- JAL-2421 -->Overview window visible region moves
2187 erratically when hidden rows or columns are present
2190 <!-- JAL-2362 -->Per-residue colourschemes applied via the
2191 Structure Viewer's colour menu don't correspond to
2195 <!-- JAL-2405 -->Protein specific colours only offered in
2196 colour and group colour menu for protein alignments
2199 <!-- JAL-2385 -->Colour threshold slider doesn't update to
2200 reflect currently selected view or group's shading
2204 <!-- JAL-2624 -->Feature colour thresholds not respected
2205 when rendered on overview and structures when opacity at
2209 <!-- JAL-2589 -->User defined gap colour not shown in
2210 overview when features overlaid on alignment
2213 <!-- JAL-2567 -->Feature settings for different views not
2214 recovered correctly from Jalview project file
2217 <!-- JAL-2256 -->Feature colours in overview when first opened
2218 (automatically via preferences) are different to the main
2222 <em>Data import/export</em>
2225 <!-- JAL-2576 -->Very large alignments take a long time to
2229 <!-- JAL-2507 -->Per-sequence RNA secondary structures
2230 added after a sequence was imported are not written to
2234 <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
2235 when importing RNA secondary structure via Stockholm
2238 <!-- JAL-2509 -->Secondary structure arrows for [] and {}
2239 not shown in correct direction for simple pseudoknots
2242 <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
2243 with lightGray or darkGray via features file (but can
2247 <!-- JAL-2383 -->Above PID colour threshold not recovered
2248 when alignment view imported from project
2251 <!-- JAL-2520,JAL-2465 -->No mappings generated between
2252 structure and sequences extracted from structure files
2253 imported via URL and viewed in Jmol
2256 <!-- JAL-2520 -->Structures loaded via URL are saved in
2257 Jalview Projects rather than fetched via URL again when
2258 the project is loaded and the structure viewed
2261 <em>Web Services</em>
2264 <!-- JAL-2519 -->EnsemblGenomes example failing after
2265 release of Ensembl v.88
2268 <!-- JAL-2366 -->Proxy server address and port always
2269 appear enabled in Preferences->Connections
2272 <!-- JAL-2461 -->DAS registry not found exceptions
2273 removed from console output
2276 <!-- JAL-2582 -->Cannot retrieve protein products from
2277 Ensembl by Peptide ID
2280 <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
2281 created from SIFTs, and spurious 'Couldn't open structure
2282 in Chimera' errors raised after April 2017 update (problem
2283 due to 'null' string rather than empty string used for
2284 residues with no corresponding PDB mapping).
2287 <em>Application UI</em>
2290 <!-- JAL-2361 -->User Defined Colours not added to Colour
2294 <!-- JAL-2401 -->Easier creation of colours for all 'Lower
2295 case' residues (button in colourscheme editor debugged and
2296 new documentation and tooltips added)
2299 <!-- JAL-2399-->Text colour threshold's 'Cancel' button
2300 doesn't restore group-specific text colour thresholds
2303 <!-- JAL-2243 -->Feature settings panel does not update as
2304 new features are added to alignment
2307 <!-- JAL-2532 -->Cancel in feature settings reverts
2308 changes to feature colours via the Amend features dialog
2311 <!-- JAL-2506 -->Null pointer exception when attempting to
2312 edit graduated feature colour via amend features dialog
2316 <!-- JAL-2436 -->Structure viewer's View -> Colour By view
2317 selection menu changes colours of alignment views
2320 <!-- JAL-2426 -->Spurious exceptions in console raised
2321 from alignment calculation workers after alignment has
2325 <!-- JAL-1608 -->Typo in selection popup menu - Create
2326 groups now 'Create Group'
2329 <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
2330 Create/Undefine group doesn't always work
2333 <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
2334 shown again after pressing 'Cancel'
2337 <!-- JAL-1256 -->Trackpad horizontal scroll gesture
2338 adjusts start position in wrap mode
2341 <!-- JAL-2563 -->Status bar doesn't show positions for
2342 ambiguous amino acids
2345 <!-- JAL-2431 -->cDNA Consensus annotation not shown in
2346 CDS/Protein view after CDS sequences added for aligned
2350 <!-- JAL-2592 -->User defined colourschemes called 'User
2351 Defined' don't appear in Colours menu
2357 <!-- JAL-2468 -->Switching between Nucleotide and Protein
2358 score models doesn't always result in an updated PCA plot
2361 <!-- JAL-2442 -->Features not rendered as transparent on
2362 overview or linked structure view
2365 <!-- JAL-2372 -->Colour group by conservation doesn't
2369 <!-- JAL-2517 -->Hitting Cancel after applying
2370 user-defined colourscheme doesn't restore original
2377 <!-- JAL-2314 -->Unit test failure:
2378 jalview.ws.jabaws.RNAStructExportImport setup fails
2381 <!-- JAL-2307 -->Unit test failure:
2382 jalview.ws.sifts.SiftsClientTest due to compatibility
2383 problems with deep array comparison equality asserts in
2384 successive versions of TestNG
2387 <!-- JAL-2479 -->Relocated StructureChooserTest and
2388 ParameterUtilsTest Unit tests to Network suite
2391 <em>New Known Issues</em>
2394 <!-- JAL-2566 -->Protein/CDS view scrolling not always in
2395 phase after a sequence motif find operation
2398 <!-- JAL-2550 -->Importing annotation file with rows
2399 containing just upper and lower case letters are
2400 interpreted as WUSS RNA secondary structure symbols
2403 <!-- JAL-2590 -->Cannot load and display Newick trees
2404 reliably from eggnog Ortholog database
2407 <!-- JAL-2468 -->Status bar shows 'Marked x columns
2408 containing features of type Highlight' when 'B' is pressed
2409 to mark columns containing highlighted regions.
2412 <!-- JAL-2321 -->Dropping a PDB file onto a sequence
2413 doesn't always add secondary structure annotation.
2418 <td width="60" nowrap>
2419 <div align="center">
2420 <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
2423 <td><div align="left">
2427 <!-- JAL-98 -->Improved memory usage: sparse arrays used
2428 for all consensus calculations
2431 <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
2434 <li>Updated Jalview's Certum code signing certificate
2437 <em>Application</em>
2440 <!-- JAL-1723 -->Sequence ID tool tip presents abridged
2441 set of database cross-references, sorted alphabetically
2444 <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
2445 from database cross references. Users with custom links
2446 will receive a <a href="webServices/urllinks.html#warning">warning
2447 dialog</a> asking them to update their preferences.
2450 <!-- JAL-2287-->Cancel button and escape listener on
2451 dialog warning user about disconnecting Jalview from a
2455 <!-- JAL-2320-->Jalview's Chimera control window closes if
2456 the Chimera it is connected to is shut down
2459 <!-- JAL-1738-->New keystroke (B) and Select highlighted
2460 columns menu item to mark columns containing highlighted
2461 regions (e.g. from structure selections or results of a
2465 <!-- JAL-2284-->Command line option for batch-generation
2466 of HTML pages rendering alignment data with the BioJS
2476 <!-- JAL-2286 -->Columns with more than one modal residue
2477 are not coloured or thresholded according to percent
2478 identity (first observed in Jalview 2.8.2)
2481 <!-- JAL-2301 -->Threonine incorrectly reported as not
2485 <!-- JAL-2318 -->Updates to documentation pages (above PID
2486 threshold, amino acid properties)
2489 <!-- JAL-2292 -->Lower case residues in sequences are not
2490 reported as mapped to residues in a structure file in the
2494 <!--JAL-2324 -->Identical features with non-numeric scores
2495 could be added multiple times to a sequence
2498 <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
2499 bond features shown as two highlighted residues rather
2500 than a range in linked structure views, and treated
2501 correctly when selecting and computing trees from features
2504 <!-- JAL-2281-->Custom URL links for database
2505 cross-references are matched to database name regardless
2510 <em>Application</em>
2513 <!-- JAL-2282-->Custom URL links for specific database
2514 names without regular expressions also offer links from
2518 <!-- JAL-2315-->Removing a single configured link in the
2519 URL links pane in Connections preferences doesn't actually
2520 update Jalview configuration
2523 <!-- JAL-2272-->CTRL-Click on a selected region to open
2524 the alignment area popup menu doesn't work on El-Capitan
2527 <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
2528 files with similarly named sequences if dropped onto the
2532 <!-- JAL-2312 -->Additional mappings are shown for PDB
2533 entries where more chains exist in the PDB accession than
2534 are reported in the SIFTS file
2537 <!-- JAL-2317-->Certain structures do not get mapped to
2538 the structure view when displayed with Chimera
2541 <!-- JAL-2317-->No chains shown in the Chimera view
2542 panel's View->Show Chains submenu
2545 <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
2546 work for wrapped alignment views
2549 <!--JAL-2197 -->Rename UI components for running JPred
2550 predictions from 'JNet' to 'JPred'
2553 <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
2554 corrupted when annotation panel vertical scroll is not at
2555 first annotation row
2558 <!--JAL-2332 -->Attempting to view structure for Hen
2559 lysozyme results in a PDB Client error dialog box
2562 <!-- JAL-2319 -->Structure View's mapping report switched
2563 ranges for PDB and sequence for SIFTS
2566 SIFTS 'Not_Observed' residues mapped to non-existant
2570 <!-- <em>New Known Issues</em>
2577 <td width="60" nowrap>
2578 <div align="center">
2579 <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
2580 <em>25/10/2016</em></strong>
2583 <td><em>Application</em>
2585 <li>3D Structure chooser opens with 'Cached structures'
2586 view if structures already loaded</li>
2587 <li>Progress bar reports models as they are loaded to
2588 structure views</li>
2594 <li>Colour by conservation always enabled and no tick
2595 shown in menu when BLOSUM or PID shading applied</li>
2596 <li>FER1_ARATH and FER2_ARATH labels were switched in
2597 example sequences/projects/trees</li>
2599 <em>Application</em>
2601 <li>Jalview projects with views of local PDB structure
2602 files saved on Windows cannot be opened on OSX</li>
2603 <li>Multiple structure views can be opened and superposed
2604 without timeout for structures with multiple models or
2605 multiple sequences in alignment</li>
2606 <li>Cannot import or associated local PDB files without a
2607 PDB ID HEADER line</li>
2608 <li>RMSD is not output in Jmol console when superposition
2610 <li>Drag and drop of URL from Browser fails for Linux and
2611 OSX versions earlier than El Capitan</li>
2612 <li>ENA client ignores invalid content from ENA server</li>
2613 <li>Exceptions are not raised in console when ENA client
2614 attempts to fetch non-existent IDs via Fetch DB Refs UI
2616 <li>Exceptions are not raised in console when a new view
2617 is created on the alignment</li>
2618 <li>OSX right-click fixed for group selections: CMD-click
2619 to insert/remove gaps in groups and CTRL-click to open group
2622 <em>Build and deployment</em>
2624 <li>URL link checker now copes with multi-line anchor
2627 <em>New Known Issues</em>
2629 <li>Drag and drop from URL links in browsers do not work
2636 <td width="60" nowrap>
2637 <div align="center">
2638 <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
2641 <td><em>General</em>
2644 <!-- JAL-2124 -->Updated Spanish translations.
2647 <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
2648 for importing structure data to Jalview. Enables mmCIF and
2652 <!-- JAL-192 --->Alignment ruler shows positions relative to
2656 <!-- JAL-2202 -->Position/residue shown in status bar when
2657 mousing over sequence associated annotation
2660 <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
2664 <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
2665 '()', canonical '[]' and invalid '{}' base pair populations
2669 <!-- JAL-2092 -->Feature settings popup menu options for
2670 showing or hiding columns containing a feature
2673 <!-- JAL-1557 -->Edit selected group by double clicking on
2674 group and sequence associated annotation labels
2677 <!-- JAL-2236 -->Sequence name added to annotation label in
2678 select/hide columns by annotation and colour by annotation
2682 </ul> <em>Application</em>
2685 <!-- JAL-2050-->Automatically hide introns when opening a
2686 gene/transcript view
2689 <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
2693 <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
2694 structure mappings with the EMBL-EBI PDBe SIFTS database
2697 <!-- JAL-2079 -->Updated download sites used for Rfam and
2698 Pfam sources to xfam.org
2701 <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
2704 <!-- JAL-2123 -->Show residue labels in Chimera when mousing
2705 over sequences in Jalview
2708 <!-- JAL-2027-->Support for reverse-complement coding
2709 regions in ENA and EMBL
2712 <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
2713 for record retrieval via ENA rest API
2716 <!-- JAL-2027 -->Support for ENA CDS records with reverse
2720 <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
2721 groovy script execution
2724 <!-- JAL-1812 -->New 'execute Groovy script' option in an
2725 alignment window's Calculate menu
2728 <!-- JAL-1812 -->Allow groovy scripts that call
2729 Jalview.getAlignFrames() to run in headless mode
2732 <!-- JAL-2068 -->Support for creating new alignment
2733 calculation workers from groovy scripts
2736 <!-- JAL-1369 --->Store/restore reference sequence in
2740 <!-- JAL-1803 -->Chain codes for a sequence's PDB
2741 associations are now saved/restored from project
2744 <!-- JAL-1993 -->Database selection dialog always shown
2745 before sequence fetcher is opened
2748 <!-- JAL-2183 -->Double click on an entry in Jalview's
2749 database chooser opens a sequence fetcher
2752 <!-- JAL-1563 -->Free-text search client for UniProt using
2753 the UniProt REST API
2756 <!-- JAL-2168 -->-nonews command line parameter to prevent
2757 the news reader opening
2760 <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
2761 querying stored in preferences
2764 <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
2768 <!-- JAL-1977-->Tooltips shown on database chooser
2771 <!-- JAL-391 -->Reverse complement function in calculate
2772 menu for nucleotide sequences
2775 <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
2776 and feature counts preserves alignment ordering (and
2777 debugged for complex feature sets).
2780 <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
2781 viewing structures with Jalview 2.10
2784 <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
2785 genome, transcript CCDS and gene ids via the Ensembl and
2786 Ensembl Genomes REST API
2789 <!-- JAL-2049 -->Protein sequence variant annotation
2790 computed for 'sequence_variant' annotation on CDS regions
2794 <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
2798 <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
2799 Ref Fetcher fails to match, or otherwise updates sequence
2800 data from external database records.
2803 <!-- JAL-2154 -->Revised Jalview Project format for
2804 efficient recovery of sequence coding and alignment
2805 annotation relationships.
2807 </ul> <!-- <em>Applet</em>
2818 <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
2822 <!-- JAL-2018-->Export features in Jalview format (again)
2823 includes graduated colourschemes
2826 <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
2827 working with big alignments and lots of hidden columns
2830 <!-- JAL-2053-->Hidden column markers not always rendered
2831 at right of alignment window
2834 <!-- JAL-2067 -->Tidied up links in help file table of
2838 <!-- JAL-2072 -->Feature based tree calculation not shown
2842 <!-- JAL-2075 -->Hidden columns ignored during feature
2843 based tree calculation
2846 <!-- JAL-2065 -->Alignment view stops updating when show
2847 unconserved enabled for group on alignment
2850 <!-- JAL-2086 -->Cannot insert gaps into sequence when
2854 <!-- JAL-2146 -->Alignment column in status incorrectly
2855 shown as "Sequence position" when mousing over
2859 <!-- JAL-2099 -->Incorrect column numbers in ruler when
2860 hidden columns present
2863 <!-- JAL-1577 -->Colour by RNA Helices not enabled when
2864 user created annotation added to alignment
2867 <!-- JAL-1841 -->RNA Structure consensus only computed for
2868 '()' base pair annotation
2871 <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
2872 in zero scores for all base pairs in RNA Structure
2876 <!-- JAL-2174-->Extend selection with columns containing
2880 <!-- JAL-2275 -->Pfam format writer puts extra space at
2881 beginning of sequence
2884 <!-- JAL-1827 -->Incomplete sequence extracted from pdb
2888 <!-- JAL-2238 -->Cannot create groups on an alignment from
2889 from a tree when t-coffee scores are shown
2892 <!-- JAL-1836,1967 -->Cannot import and view PDB
2893 structures with chains containing negative resnums (4q4h)
2896 <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
2900 <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
2901 to Clustal, PIR and PileUp output
2904 <!-- JAL-2008 -->Reordering sequence features that are
2905 not visible causes alignment window to repaint
2908 <!-- JAL-2006 -->Threshold sliders don't work in
2909 graduated colour and colour by annotation row for e-value
2910 scores associated with features and annotation rows
2913 <!-- JAL-1797 -->amino acid physicochemical conservation
2914 calculation should be case independent
2917 <!-- JAL-2173 -->Remove annotation also updates hidden
2921 <!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
2922 example file (uniref50.fa, feredoxin.fa, unaligned.fa,
2923 exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
2926 <!-- JAL-2065 -->Null pointer exceptions and redraw
2927 problems when reference sequence defined and 'show
2928 non-conserved' enabled
2931 <!-- JAL-1306 -->Quality and Conservation are now shown on
2932 load even when Consensus calculation is disabled
2935 <!-- JAL-1932 -->Remove right on penultimate column of
2936 alignment does nothing
2939 <em>Application</em>
2942 <!-- JAL-1552-->URLs and links can't be imported by
2943 drag'n'drop on OSX when launched via webstart (note - not
2944 yet fixed for El Capitan)
2947 <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
2948 output when running on non-gb/us i18n platforms
2951 <!-- JAL-1944 -->Error thrown when exporting a view with
2952 hidden sequences as flat-file alignment
2955 <!-- JAL-2030-->InstallAnywhere distribution fails when
2959 <!-- JAL-2080-->Jalview very slow to launch via webstart
2960 (also hotfix for 2.9.0b2)
2963 <!-- JAL-2085 -->Cannot save project when view has a
2964 reference sequence defined
2967 <!-- JAL-1011 -->Columns are suddenly selected in other
2968 alignments and views when revealing hidden columns
2971 <!-- JAL-1989 -->Hide columns not mirrored in complement
2972 view in a cDNA/Protein splitframe
2975 <!-- JAL-1369 -->Cannot save/restore representative
2976 sequence from project when only one sequence is
2980 <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
2981 in Structure Chooser
2984 <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
2985 structure consensus didn't refresh annotation panel
2988 <!-- JAL-1962 -->View mapping in structure view shows
2989 mappings between sequence and all chains in a PDB file
2992 <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
2993 dialogs format columns correctly, don't display array
2994 data, sort columns according to type
2997 <!-- JAL-1975 -->Export complete shown after destination
2998 file chooser is cancelled during an image export
3001 <!-- JAL-2025 -->Error when querying PDB Service with
3002 sequence name containing special characters
3005 <!-- JAL-2024 -->Manual PDB structure querying should be
3009 <!-- JAL-2104 -->Large tooltips with broken HTML
3010 formatting don't wrap
3013 <!-- JAL-1128 -->Figures exported from wrapped view are
3014 truncated so L looks like I in consensus annotation
3017 <!-- JAL-2003 -->Export features should only export the
3018 currently displayed features for the current selection or
3022 <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
3023 after fetching cross-references, and restoring from
3027 <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
3028 followed in the structure viewer
3031 <!-- JAL-2163 -->Titles for individual alignments in
3032 splitframe not restored from project
3035 <!-- JAL-2145 -->missing autocalculated annotation at
3036 trailing end of protein alignment in transcript/product
3037 splitview when pad-gaps not enabled by default
3040 <!-- JAL-1797 -->amino acid physicochemical conservation
3044 <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
3045 article has been read (reopened issue due to
3046 internationalisation problems)
3049 <!-- JAL-1960 -->Only offer PDB structures in structure
3050 viewer based on sequence name, PDB and UniProt
3055 <!-- JAL-1976 -->No progress bar shown during export of
3059 <!-- JAL-2213 -->Structures not always superimposed after
3060 multiple structures are shown for one or more sequences.
3063 <!-- JAL-1370 -->Reference sequence characters should not
3064 be replaced with '.' when 'Show unconserved' format option
3068 <!-- JAL-1823 -->Cannot specify chain code when entering
3069 specific PDB id for sequence
3072 <!-- JAL-1944 -->File->Export->.. as doesn't work when
3073 'Export hidden sequences' is enabled, but 'export hidden
3074 columns' is disabled.
3077 <!--JAL-2026-->Best Quality option in structure chooser
3078 selects lowest rather than highest resolution structures
3082 <!-- JAL-1887 -->Incorrect start and end reported for PDB
3083 to sequence mapping in 'View Mappings' report
3086 <!-- JAL-2284 -->Unable to read old Jalview projects that
3087 contain non-XML data added after Jalvew wrote project.
3090 <!-- JAL-2118 -->Newly created annotation row reorders
3091 after clicking on it to create new annotation for a
3095 <!-- JAL-1980 -->Null Pointer Exception raised when
3096 pressing Add on an orphaned cut'n'paste window.
3098 <!-- may exclude, this is an external service stability issue JAL-1941
3099 -- > RNA 3D structure not added via DSSR service</li> -->
3104 <!-- JAL-2151 -->Incorrect columns are selected when
3105 hidden columns present before start of sequence
3108 <!-- JAL-1986 -->Missing dependencies on applet pages
3112 <!-- JAL-1947 -->Overview pixel size changes when
3113 sequences are hidden in applet
3116 <!-- JAL-1996 -->Updated instructions for applet
3117 deployment on examples pages.
3124 <td width="60" nowrap>
3125 <div align="center">
3126 <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
3127 <em>16/10/2015</em></strong>
3130 <td><em>General</em>
3132 <li>Time stamps for signed Jalview application and applet
3137 <em>Application</em>
3139 <li>Duplicate group consensus and conservation rows
3140 shown when tree is partitioned</li>
3141 <li>Erratic behaviour when tree partitions made with
3142 multiple cDNA/Protein split views</li>
3148 <td width="60" nowrap>
3149 <div align="center">
3150 <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
3151 <em>8/10/2015</em></strong>
3154 <td><em>General</em>
3156 <li>Updated Spanish translations of localized text for
3158 </ul> <em>Application</em>
3160 <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
3161 <li>Signed OSX InstallAnywhere installer<br></li>
3162 <li>Support for per-sequence based annotations in BioJSON</li>
3163 </ul> <em>Applet</em>
3165 <li>Split frame example added to applet examples page</li>
3166 </ul> <em>Build and Deployment</em>
3169 <!-- JAL-1888 -->New ant target for running Jalview's test
3177 <li>Mapping of cDNA to protein in split frames
3178 incorrect when sequence start > 1</li>
3179 <li>Broken images in filter column by annotation dialog
3181 <li>Feature colours not parsed from features file</li>
3182 <li>Exceptions and incomplete link URLs recovered when
3183 loading a features file containing HTML tags in feature
3187 <em>Application</em>
3189 <li>Annotations corrupted after BioJS export and
3191 <li>Incorrect sequence limits after Fetch DB References
3192 with 'trim retrieved sequences'</li>
3193 <li>Incorrect warning about deleting all data when
3194 deleting selected columns</li>
3195 <li>Patch to build system for shipping properly signed
3196 JNLP templates for webstart launch</li>
3197 <li>EMBL-PDBe fetcher/viewer dialogs do not offer
3198 unreleased structures for download or viewing</li>
3199 <li>Tab/space/return keystroke operation of EMBL-PDBe
3200 fetcher/viewer dialogs works correctly</li>
3201 <li>Disabled 'minimise' button on Jalview windows
3202 running on OSX to workaround redraw hang bug</li>
3203 <li>Split cDNA/Protein view position and geometry not
3204 recovered from jalview project</li>
3205 <li>Initial enabled/disabled state of annotation menu
3206 sorter 'show autocalculated first/last' corresponds to
3208 <li>Restoring of Clustal, RNA Helices and T-Coffee
3209 color schemes from BioJSON</li>
3213 <li>Reorder sequences mirrored in cDNA/Protein split
3215 <li>Applet with Jmol examples not loading correctly</li>
3221 <td><div align="center">
3222 <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
3224 <td><em>General</em>
3226 <li>Linked visualisation and analysis of DNA and Protein
3229 <li>Translated cDNA alignments shown as split protein
3230 and DNA alignment views</li>
3231 <li>Codon consensus annotation for linked protein and
3232 cDNA alignment views</li>
3233 <li>Link cDNA or Protein product sequences by loading
3234 them onto Protein or cDNA alignments</li>
3235 <li>Reconstruct linked cDNA alignment from aligned
3236 protein sequences</li>
3239 <li>Jmol integration updated to Jmol v14.2.14</li>
3240 <li>Import and export of Jalview alignment views as <a
3241 href="features/bioJsonFormat.html">BioJSON</a></li>
3242 <li>New alignment annotation file statements for
3243 reference sequences and marking hidden columns</li>
3244 <li>Reference sequence based alignment shading to
3245 highlight variation</li>
3246 <li>Select or hide columns according to alignment
3248 <li>Find option for locating sequences by description</li>
3249 <li>Conserved physicochemical properties shown in amino
3250 acid conservation row</li>
3251 <li>Alignments can be sorted by number of RNA helices</li>
3252 </ul> <em>Application</em>
3254 <li>New cDNA/Protein analysis capabilities
3256 <li>Get Cross-References should open a Split Frame
3257 view with cDNA/Protein</li>
3258 <li>Detect when nucleotide sequences and protein
3259 sequences are placed in the same alignment</li>
3260 <li>Split cDNA/Protein views are saved in Jalview
3265 <li>Use REST API to talk to Chimera</li>
3266 <li>Selected regions in Chimera are highlighted in linked
3267 Jalview windows</li>
3269 <li>VARNA RNA viewer updated to v3.93</li>
3270 <li>VARNA views are saved in Jalview Projects</li>
3271 <li>Pseudoknots displayed as Jalview RNA annotation can
3272 be shown in VARNA</li>
3274 <li>Make groups for selection uses marked columns as well
3275 as the active selected region</li>
3277 <li>Calculate UPGMA and NJ trees using sequence feature
3279 <li>New Export options
3281 <li>New Export Settings dialog to control hidden
3282 region export in flat file generation</li>
3284 <li>Export alignment views for display with the <a
3285 href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
3287 <li>Export scrollable SVG in HTML page</li>
3288 <li>Optional embedding of BioJSON data when exporting
3289 alignment figures to HTML</li>
3291 <li>3D structure retrieval and display
3293 <li>Free text and structured queries with the PDBe
3295 <li>PDBe Search API based discovery and selection of
3296 PDB structures for a sequence set</li>
3300 <li>JPred4 employed for protein secondary structure
3302 <li>Hide Insertions menu option to hide unaligned columns
3303 for one or a group of sequences</li>
3304 <li>Automatically hide insertions in alignments imported
3305 from the JPred4 web server</li>
3306 <li>(Nearly) Native 'Quaqua' dialogs for browsing file
3307 system on OSX<br />LGPL libraries courtesy of <a
3308 href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
3310 <li>changed 'View nucleotide structure' submenu to 'View
3311 VARNA 2D Structure'</li>
3312 <li>change "View protein structure" menu option to "3D
3315 </ul> <em>Applet</em>
3317 <li>New layout for applet example pages</li>
3318 <li>New parameters to enable SplitFrame view
3319 (file2,enableSplitFrame, scaleProteinAsCdna)</li>
3320 <li>New example demonstrating linked viewing of cDNA and
3321 Protein alignments</li>
3322 </ul> <em>Development and deployment</em>
3324 <li>Java 1.7 minimum requirement for Jalview 2.9</li>
3325 <li>Include installation type and git revision in build
3326 properties and console log output</li>
3327 <li>Jalview Github organisation, and new github site for
3328 storing BioJsMSA Templates</li>
3329 <li>Jalview's unit tests now managed with TestNG</li>
3332 <!-- <em>General</em>
3334 </ul> --> <!-- issues resolved --> <em>Application</em>
3336 <li>Escape should close any open find dialogs</li>
3337 <li>Typo in select-by-features status report</li>
3338 <li>Consensus RNA secondary secondary structure
3339 predictions are not highlighted in amber</li>
3340 <li>Missing gap character in v2.7 example file means
3341 alignment appears unaligned when pad-gaps is not enabled</li>
3342 <li>First switch to RNA Helices colouring doesn't colour
3343 associated structure views</li>
3344 <li>ID width preference option is greyed out when auto
3345 width checkbox not enabled</li>
3346 <li>Stopped a warning dialog from being shown when
3347 creating user defined colours</li>
3348 <li>'View Mapping' in structure viewer shows sequence
3349 mappings for just that viewer's sequences</li>
3350 <li>Workaround for superposing PDB files containing
3351 multiple models in Chimera</li>
3352 <li>Report sequence position in status bar when hovering
3353 over Jmol structure</li>
3354 <li>Cannot output gaps as '.' symbols with Selection ->
3355 output to text box</li>
3356 <li>Flat file exports of alignments with hidden columns
3357 have incorrect sequence start/end</li>
3358 <li>'Aligning' a second chain to a Chimera structure from
3360 <li>Colour schemes applied to structure viewers don't
3361 work for nucleotide</li>
3362 <li>Loading/cut'n'pasting an empty or invalid file leads
3363 to a grey/invisible alignment window</li>
3364 <li>Exported Jpred annotation from a sequence region
3365 imports to different position</li>
3366 <li>Space at beginning of sequence feature tooltips shown
3367 on some platforms</li>
3368 <li>Chimera viewer 'View | Show Chain' menu is not
3370 <li>'New View' fails with a Null Pointer Exception in
3371 console if Chimera has been opened</li>
3372 <li>Mouseover to Chimera not working</li>
3373 <li>Miscellaneous ENA XML feature qualifiers not
3375 <li>NPE in annotation renderer after 'Extract Scores'</li>
3376 <li>If two structures in one Chimera window, mouseover of
3377 either sequence shows on first structure</li>
3378 <li>'Show annotations' options should not make
3379 non-positional annotations visible</li>
3380 <li>Subsequence secondary structure annotation not shown
3381 in right place after 'view flanking regions'</li>
3382 <li>File Save As type unset when current file format is
3384 <li>Save as '.jar' option removed for saving Jalview
3386 <li>Colour by Sequence colouring in Chimera more
3388 <li>Cannot 'add reference annotation' for a sequence in
3389 several views on same alignment</li>
3390 <li>Cannot show linked products for EMBL / ENA records</li>
3391 <li>Jalview's tooltip wraps long texts containing no
3393 </ul> <em>Applet</em>
3395 <li>Jmol to JalviewLite mouseover/link not working</li>
3396 <li>JalviewLite can't import sequences with ID
3397 descriptions containing angle brackets</li>
3398 </ul> <em>General</em>
3400 <li>Cannot export and reimport RNA secondary structure
3401 via jalview annotation file</li>
3402 <li>Random helix colour palette for colour by annotation
3403 with RNA secondary structure</li>
3404 <li>Mouseover to cDNA from STOP residue in protein
3405 translation doesn't work.</li>
3406 <li>hints when using the select by annotation dialog box</li>
3407 <li>Jmol alignment incorrect if PDB file has alternate CA
3409 <li>FontChooser message dialog appears to hang after
3410 choosing 1pt font</li>
3411 <li>Peptide secondary structure incorrectly imported from
3412 annotation file when annotation display text includes 'e' or
3414 <li>Cannot set colour of new feature type whilst creating
3416 <li>cDNA translation alignment should not be sequence
3417 order dependent</li>
3418 <li>'Show unconserved' doesn't work for lower case
3420 <li>Nucleotide ambiguity codes involving R not recognised</li>
3421 </ul> <em>Deployment and Documentation</em>
3423 <li>Applet example pages appear different to the rest of
3424 www.jalview.org</li>
3425 </ul> <em>Application Known issues</em>
3427 <li>Incomplete sequence extracted from PDB entry 3a6s</li>
3428 <li>Misleading message appears after trying to delete
3430 <li>Jalview icon not shown in dock after InstallAnywhere
3431 version launches</li>
3432 <li>Fetching EMBL reference for an RNA sequence results
3433 fails with a sequence mismatch</li>
3434 <li>Corrupted or unreadable alignment display when
3435 scrolling alignment to right</li>
3436 <li>ArrayIndexOutOfBoundsException thrown when remove
3437 empty columns called on alignment with ragged gapped ends</li>
3438 <li>auto calculated alignment annotation rows do not get
3439 placed above or below non-autocalculated rows</li>
3440 <li>Jalview dekstop becomes sluggish at full screen in
3441 ultra-high resolution</li>
3442 <li>Cannot disable consensus calculation independently of
3443 quality and conservation</li>
3444 <li>Mouseover highlighting between cDNA and protein can
3445 become sluggish with more than one splitframe shown</li>
3446 </ul> <em>Applet Known Issues</em>
3448 <li>Core PDB parsing code requires Jmol</li>
3449 <li>Sequence canvas panel goes white when alignment
3450 window is being resized</li>
3456 <td><div align="center">
3457 <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
3459 <td><em>General</em>
3461 <li>Updated Java code signing certificate donated by
3463 <li>Features and annotation preserved when performing
3464 pairwise alignment</li>
3465 <li>RNA pseudoknot annotation can be
3466 imported/exported/displayed</li>
3467 <li>'colour by annotation' can colour by RNA and
3468 protein secondary structure</li>
3469 <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
3470 post-hoc with 2.9 release</em>)
3473 </ul> <em>Application</em>
3475 <li>Extract and display secondary structure for sequences
3476 with 3D structures</li>
3477 <li>Support for parsing RNAML</li>
3478 <li>Annotations menu for layout
3480 <li>sort sequence annotation rows by alignment</li>
3481 <li>place sequence annotation above/below alignment
3484 <li>Output in Stockholm format</li>
3485 <li>Internationalisation: improved Spanish (es)
3487 <li>Structure viewer preferences tab</li>
3488 <li>Disorder and Secondary Structure annotation tracks
3489 shared between alignments</li>
3490 <li>UCSF Chimera launch and linked highlighting from
3492 <li>Show/hide all sequence associated annotation rows for
3493 all or current selection</li>
3494 <li>disorder and secondary structure predictions
3495 available as dataset annotation</li>
3496 <li>Per-sequence rna helices colouring</li>
3499 <li>Sequence database accessions imported when fetching
3500 alignments from Rfam</li>
3501 <li>update VARNA version to 3.91</li>
3503 <li>New groovy scripts for exporting aligned positions,
3504 conservation values, and calculating sum of pairs scores.</li>
3505 <li>Command line argument to set default JABAWS server</li>
3506 <li>include installation type in build properties and
3507 console log output</li>
3508 <li>Updated Jalview project format to preserve dataset
3512 <!-- issues resolved --> <em>Application</em>
3514 <li>Distinguish alignment and sequence associated RNA
3515 structure in structure->view->VARNA</li>
3516 <li>Raise dialog box if user deletes all sequences in an
3518 <li>Pressing F1 results in documentation opening twice</li>
3519 <li>Sequence feature tooltip is wrapped</li>
3520 <li>Double click on sequence associated annotation
3521 selects only first column</li>
3522 <li>Redundancy removal doesn't result in unlinked
3523 leaves shown in tree</li>
3524 <li>Undos after several redundancy removals don't undo
3526 <li>Hide sequence doesn't hide associated annotation</li>
3527 <li>User defined colours dialog box too big to fit on
3528 screen and buttons not visible</li>
3529 <li>author list isn't updated if already written to
3530 Jalview properties</li>
3531 <li>Popup menu won't open after retrieving sequence
3533 <li>File open window for associate PDB doesn't open</li>
3534 <li>Left-then-right click on a sequence id opens a
3535 browser search window</li>
3536 <li>Cannot open sequence feature shading/sort popup menu
3537 in feature settings dialog</li>
3538 <li>better tooltip placement for some areas of Jalview
3540 <li>Allow addition of JABAWS Server which doesn't
3541 pass validation</li>
3542 <li>Web services parameters dialog box is too large to
3544 <li>Muscle nucleotide alignment preset obscured by
3546 <li>JABAWS preset submenus don't contain newly
3547 defined user preset</li>
3548 <li>MSA web services warns user if they were launched
3549 with invalid input</li>
3550 <li>Jalview cannot contact DAS Registy when running on
3553 <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
3554 'Superpose with' submenu not shown when new view
3558 </ul> <!-- <em>Applet</em>
3560 </ul> <em>General</em>
3562 </ul>--> <em>Deployment and Documentation</em>
3564 <li>2G and 1G options in launchApp have no effect on
3565 memory allocation</li>
3566 <li>launchApp service doesn't automatically open
3567 www.jalview.org/examples/exampleFile.jar if no file is given</li>
3569 <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
3570 InstallAnywhere reports cannot find valid JVM when Java
3571 1.7_055 is available
3573 </ul> <em>Application Known issues</em>
3576 <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
3577 corrupted or unreadable alignment display when scrolling
3581 <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
3582 retrieval fails but progress bar continues for DAS retrieval
3583 with large number of ID
3586 <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
3587 flatfile output of visible region has incorrect sequence
3591 <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
3592 rna structure consensus doesn't update when secondary
3593 structure tracks are rearranged
3596 <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
3597 invalid rna structure positional highlighting does not
3598 highlight position of invalid base pairs
3601 <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
3602 out of memory errors are not raised when saving Jalview
3603 project from alignment window file menu
3606 <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
3607 Switching to RNA Helices colouring doesn't propagate to
3611 <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
3612 colour by RNA Helices not enabled when user created
3613 annotation added to alignment
3616 <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
3617 Jalview icon not shown on dock in Mountain Lion/Webstart
3619 </ul> <em>Applet Known Issues</em>
3622 <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
3623 JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
3626 <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
3627 Jalview and Jmol example not compatible with IE9
3630 <li>Sort by annotation score doesn't reverse order
3636 <td><div align="center">
3637 <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
3640 <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
3643 <li>Internationalisation of user interface (usually
3644 called i18n support) and translation for Spanish locale</li>
3645 <li>Define/Undefine group on current selection with
3646 Ctrl-G/Shift Ctrl-G</li>
3647 <li>Improved group creation/removal options in
3648 alignment/sequence Popup menu</li>
3649 <li>Sensible precision for symbol distribution
3650 percentages shown in logo tooltip.</li>
3651 <li>Annotation panel height set according to amount of
3652 annotation when alignment first opened</li>
3653 </ul> <em>Application</em>
3655 <li>Interactive consensus RNA secondary structure
3656 prediction VIENNA RNAAliFold JABA 2.1 service</li>
3657 <li>Select columns containing particular features from
3658 Feature Settings dialog</li>
3659 <li>View all 'representative' PDB structures for selected
3661 <li>Update Jalview project format:
3663 <li>New file extension for Jalview projects '.jvp'</li>
3664 <li>Preserve sequence and annotation dataset (to
3665 store secondary structure annotation,etc)</li>
3666 <li>Per group and alignment annotation and RNA helix
3670 <li>New similarity measures for PCA and Tree calculation
3672 <li>Experimental support for retrieval and viewing of
3673 flanking regions for an alignment</li>
3677 <!-- issues resolved --> <em>Application</em>
3679 <li>logo keeps spinning and status remains at queued or
3680 running after job is cancelled</li>
3681 <li>cannot export features from alignments imported from
3682 Jalview/VAMSAS projects</li>
3683 <li>Buggy slider for web service parameters that take
3685 <li>Newly created RNA secondary structure line doesn't
3686 have 'display all symbols' flag set</li>
3687 <li>T-COFFEE alignment score shading scheme and other
3688 annotation shading not saved in Jalview project</li>
3689 <li>Local file cannot be loaded in freshly downloaded
3691 <li>Jalview icon not shown on dock in Mountain
3693 <li>Load file from desktop file browser fails</li>
3694 <li>Occasional NPE thrown when calculating large trees</li>
3695 <li>Cannot reorder or slide sequences after dragging an
3696 alignment onto desktop</li>
3697 <li>Colour by annotation dialog throws NPE after using
3698 'extract scores' function</li>
3699 <li>Loading/cut'n'pasting an empty file leads to a grey
3700 alignment window</li>
3701 <li>Disorder thresholds rendered incorrectly after
3702 performing IUPred disorder prediction</li>
3703 <li>Multiple group annotated consensus rows shown when
3704 changing 'normalise logo' display setting</li>
3705 <li>Find shows blank dialog after 'finished searching' if
3706 nothing matches query</li>
3707 <li>Null Pointer Exceptions raised when sorting by
3708 feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
3710 <li>Errors in Jmol console when structures in alignment
3711 don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
3713 <li>Not all working JABAWS services are shown in
3715 <li>JAVAWS version of Jalview fails to launch with
3716 'invalid literal/length code'</li>
3717 <li>Annotation/RNA Helix colourschemes cannot be applied
3718 to alignment with groups (actually fixed in 2.8.0b1)</li>
3719 <li>RNA Helices and T-Coffee Scores available as default
3722 </ul> <em>Applet</em>
3724 <li>Remove group option is shown even when selection is
3726 <li>Apply to all groups ticked but colourscheme changes
3727 don't affect groups</li>
3728 <li>Documented RNA Helices and T-Coffee Scores as valid
3729 colourscheme name</li>
3730 <li>Annotation labels drawn on sequence IDs when
3731 Annotation panel is not displayed</li>
3732 <li>Increased font size for dropdown menus on OSX and
3733 embedded windows</li>
3734 </ul> <em>Other</em>
3736 <li>Consensus sequence for alignments/groups with a
3737 single sequence were not calculated</li>
3738 <li>annotation files that contain only groups imported as
3739 annotation and junk sequences</li>
3740 <li>Fasta files with sequences containing '*' incorrectly
3741 recognised as PFAM or BLC</li>
3742 <li>conservation/PID slider apply all groups option
3743 doesn't affect background (2.8.0b1)
3745 <li>redundancy highlighting is erratic at 0% and 100%</li>
3746 <li>Remove gapped columns fails for sequences with ragged
3748 <li>AMSA annotation row with leading spaces is not
3749 registered correctly on import</li>
3750 <li>Jalview crashes when selecting PCA analysis for
3751 certain alignments</li>
3752 <li>Opening the colour by annotation dialog for an
3753 existing annotation based 'use original colours'
3754 colourscheme loses original colours setting</li>
3759 <td><div align="center">
3760 <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
3761 <em>30/1/2014</em></strong>
3765 <li>Trusted certificates for JalviewLite applet and
3766 Jalview Desktop application<br />Certificate was donated by
3767 <a href="https://www.certum.eu">Certum</a> to the Jalview
3768 open source project).
3770 <li>Jalview SRS links replaced by UniProt and EBI-search</li>
3771 <li>Output in Stockholm format</li>
3772 <li>Allow import of data from gzipped files</li>
3773 <li>Export/import group and sequence associated line
3774 graph thresholds</li>
3775 <li>Nucleotide substitution matrix that supports RNA and
3776 ambiguity codes</li>
3777 <li>Allow disorder predictions to be made on the current
3778 selection (or visible selection) in the same way that JPred
3780 <li>Groovy scripting for headless Jalview operation</li>
3781 </ul> <em>Other improvements</em>
3783 <li>Upgrade desktop installer to InstallAnywhere 2013</li>
3784 <li>COMBINE statement uses current SEQUENCE_REF and
3785 GROUP_REF scope to group annotation rows</li>
3786 <li>Support '' style escaping of quotes in Newick
3788 <li>Group options for JABAWS service by command line name</li>
3789 <li>Empty tooltip shown for JABA service options with a
3790 link but no description</li>
3791 <li>Select primary source when selecting authority in
3792 database fetcher GUI</li>
3793 <li>Add .mfa to FASTA file extensions recognised by
3795 <li>Annotation label tooltip text wrap</li>
3800 <li>Slow scrolling when lots of annotation rows are
3802 <li>Lots of NPE (and slowness) after creating RNA
3803 secondary structure annotation line</li>
3804 <li>Sequence database accessions not imported when
3805 fetching alignments from Rfam</li>
3806 <li>Incorrect SHMR submission for sequences with
3808 <li>View all structures does not always superpose
3810 <li>Option widgets in service parameters not updated to
3811 reflect user or preset settings</li>
3812 <li>Null pointer exceptions for some services without
3813 presets or adjustable parameters</li>
3814 <li>Discover PDB IDs entry in structure menu doesn't
3815 discover PDB xRefs</li>
3816 <li>Exception encountered while trying to retrieve
3817 features with DAS</li>
3818 <li>Lowest value in annotation row isn't coloured
3819 when colour by annotation (per sequence) is coloured</li>
3820 <li>Keyboard mode P jumps to start of gapped region when
3821 residue follows a gap</li>
3822 <li>Jalview appears to hang importing an alignment with
3823 Wrap as default or after enabling Wrap</li>
3824 <li>'Right click to add annotations' message
3825 shown in wrap mode when no annotations present</li>
3826 <li>Disorder predictions fail with NPE if no automatic
3827 annotation already exists on alignment</li>
3828 <li>oninit javascript function should be called after
3829 initialisation completes</li>
3830 <li>Remove redundancy after disorder prediction corrupts
3831 alignment window display</li>
3832 <li>Example annotation file in documentation is invalid</li>
3833 <li>Grouped line graph annotation rows are not exported
3834 to annotation file</li>
3835 <li>Multi-harmony analysis cannot be run when only two
3837 <li>Cannot create multiple groups of line graphs with
3838 several 'combine' statements in annotation file</li>
3839 <li>Pressing return several times causes Number Format
3840 exceptions in keyboard mode</li>
3841 <li>Multi-harmony (SHMMR) method doesn't submit
3842 correct partitions for input data</li>
3843 <li>Translation from DNA to Amino Acids fails</li>
3844 <li>Jalview fail to load newick tree with quoted label</li>
3845 <li>--headless flag isn't understood</li>
3846 <li>ClassCastException when generating EPS in headless
3848 <li>Adjusting sequence-associated shading threshold only
3849 changes one row's threshold</li>
3850 <li>Preferences and Feature settings panel panel
3851 doesn't open</li>
3852 <li>hide consensus histogram also hides conservation and
3853 quality histograms</li>
3858 <td><div align="center">
3859 <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
3861 <td><em>Application</em>
3863 <li>Support for JABAWS 2.0 Services (AACon alignment
3864 conservation, protein disorder and Clustal Omega)</li>
3865 <li>JABAWS server status indicator in Web Services
3867 <li>VARNA (http://varna.lri.fr) viewer for RNA structures
3868 in Jalview alignment window</li>
3869 <li>Updated Jalview build and deploy framework for OSX
3870 mountain lion, windows 7, and 8</li>
3871 <li>Nucleotide substitution matrix for PCA that supports
3872 RNA and ambiguity codes</li>
3874 <li>Improved sequence database retrieval GUI</li>
3875 <li>Support fetching and database reference look up
3876 against multiple DAS sources (Fetch all from in 'fetch db
3878 <li>Jalview project improvements
3880 <li>Store and retrieve the 'belowAlignment'
3881 flag for annotation</li>
3882 <li>calcId attribute to group annotation rows on the
3884 <li>Store AACon calculation settings for a view in
3885 Jalview project</li>
3889 <li>horizontal scrolling gesture support</li>
3890 <li>Visual progress indicator when PCA calculation is
3892 <li>Simpler JABA web services menus</li>
3893 <li>visual indication that web service results are still
3894 being retrieved from server</li>
3895 <li>Serialise the dialogs that are shown when Jalview
3896 starts up for first time</li>
3897 <li>Jalview user agent string for interacting with HTTP
3899 <li>DAS 1.6 and DAS 2.0 source support using new JDAS
3901 <li>Examples directory and Groovy library included in
3902 InstallAnywhere distribution</li>
3903 </ul> <em>Applet</em>
3905 <li>RNA alignment and secondary structure annotation
3906 visualization applet example</li>
3907 </ul> <em>General</em>
3909 <li>Normalise option for consensus sequence logo</li>
3910 <li>Reset button in PCA window to return dimensions to
3912 <li>Allow seqspace or Jalview variant of alignment PCA
3914 <li>PCA with either nucleic acid and protein substitution
3916 <li>Allow windows containing HTML reports to be exported
3918 <li>Interactive display and editing of RNA secondary
3919 structure contacts</li>
3920 <li>RNA Helix Alignment Colouring</li>
3921 <li>RNA base pair logo consensus</li>
3922 <li>Parse sequence associated secondary structure
3923 information in Stockholm files</li>
3924 <li>HTML Export database accessions and annotation
3925 information presented in tooltip for sequences</li>
3926 <li>Import secondary structure from LOCARNA clustalw
3927 style RNA alignment files</li>
3928 <li>import and visualise T-COFFEE quality scores for an
3930 <li>'colour by annotation' per sequence option to
3931 shade each sequence according to its associated alignment
3933 <li>New Jalview Logo</li>
3934 </ul> <em>Documentation and Development</em>
3936 <li>documentation for score matrices used in Jalview</li>
3937 <li>New Website!</li>
3939 <td><em>Application</em>
3941 <li>PDB, Unprot and EMBL (ENA) databases retrieved via
3942 wsdbfetch REST service</li>
3943 <li>Stop windows being moved outside desktop on OSX</li>
3944 <li>Filetype associations not installed for webstart
3946 <li>Jalview does not always retrieve progress of a JABAWS
3947 job execution in full once it is complete</li>
3948 <li>revise SHMR RSBS definition to ensure alignment is
3949 uploaded via ali_file parameter</li>
3950 <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
3951 <li>View all structures superposed fails with exception</li>
3952 <li>Jnet job queues forever if a very short sequence is
3953 submitted for prediction</li>
3954 <li>Cut and paste menu not opened when mouse clicked on
3956 <li>Putting fractional value into integer text box in
3957 alignment parameter dialog causes Jalview to hang</li>
3958 <li>Structure view highlighting doesn't work on
3960 <li>View all structures fails with exception shown in
3962 <li>Characters in filename associated with PDBEntry not
3963 escaped in a platform independent way</li>
3964 <li>Jalview desktop fails to launch with exception when
3966 <li>Tree calculation reports 'you must have 2 or more
3967 sequences selected' when selection is empty</li>
3968 <li>Jalview desktop fails to launch with jar signature
3969 failure when java web start temporary file caching is
3971 <li>DAS Sequence retrieval with range qualification
3972 results in sequence xref which includes range qualification</li>
3973 <li>Errors during processing of command line arguments
3974 cause progress bar (JAL-898) to be removed</li>
3975 <li>Replace comma for semi-colon option not disabled for
3976 DAS sources in sequence fetcher</li>
3977 <li>Cannot close news reader when JABAWS server warning
3978 dialog is shown</li>
3979 <li>Option widgets not updated to reflect user settings</li>
3980 <li>Edited sequence not submitted to web service</li>
3981 <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
3982 <li>InstallAnywhere installer doesn't unpack and run
3983 on OSX Mountain Lion</li>
3984 <li>Annotation panel not given a scroll bar when
3985 sequences with alignment annotation are pasted into the
3987 <li>Sequence associated annotation rows not associated
3988 when loaded from Jalview project</li>
3989 <li>Browser launch fails with NPE on java 1.7</li>
3990 <li>JABAWS alignment marked as finished when job was
3991 cancelled or job failed due to invalid input</li>
3992 <li>NPE with v2.7 example when clicking on Tree
3993 associated with all views</li>
3994 <li>Exceptions when copy/paste sequences with grouped
3995 annotation rows to new window</li>
3996 </ul> <em>Applet</em>
3998 <li>Sequence features are momentarily displayed before
3999 they are hidden using hidefeaturegroups applet parameter</li>
4000 <li>loading features via javascript API automatically
4001 enables feature display</li>
4002 <li>scrollToColumnIn javascript API method doesn't
4004 </ul> <em>General</em>
4006 <li>Redundancy removal fails for rna alignment</li>
4007 <li>PCA calculation fails when sequence has been selected
4008 and then deselected</li>
4009 <li>PCA window shows grey box when first opened on OSX</li>
4010 <li>Letters coloured pink in sequence logo when alignment
4011 coloured with clustalx</li>
4012 <li>Choosing fonts without letter symbols defined causes
4013 exceptions and redraw errors</li>
4014 <li>Initial PCA plot view is not same as manually
4015 reconfigured view</li>
4016 <li>Grouped annotation graph label has incorrect line
4018 <li>Grouped annotation graph label display is corrupted
4019 for lots of labels</li>
4024 <div align="center">
4025 <strong><a name="Jalview2.7">2.7</a> </strong><br> <em>27/09/2011</em>
4028 <td><em>Application</em>
4030 <li>Jalview Desktop News Reader</li>
4031 <li>Tweaked default layout of web services menu</li>
4032 <li>View/alignment association menu to enable user to
4033 easily specify which alignment a multi-structure view takes
4034 its colours/correspondences from</li>
4035 <li>Allow properties file location to be specified as URL</li>
4036 <li>Extend Jalview project to preserve associations
4037 between many alignment views and a single Jmol display</li>
4038 <li>Store annotation row height in Jalview project file</li>
4039 <li>Annotation row column label formatting attributes
4040 stored in project file</li>
4041 <li>Annotation row order for auto-calculated annotation
4042 rows preserved in Jalview project file</li>
4043 <li>Visual progress indication when Jalview state is
4044 saved using Desktop window menu</li>
4045 <li>Visual indication that command line arguments are
4046 still being processed</li>
4047 <li>Groovy script execution from URL</li>
4048 <li>Colour by annotation default min and max colours in
4050 <li>Automatically associate PDB files dragged onto an
4051 alignment with sequences that have high similarity and
4053 <li>Update JGoogleAnalytics to latest release (0.3)</li>
4054 <li>'view structures' option to open many
4055 structures in same window</li>
4056 <li>Sort associated views menu option for tree panel</li>
4057 <li>Group all JABA and non-JABA services for a particular
4058 analysis function in its own submenu</li>
4059 </ul> <em>Applet</em>
4061 <li>Userdefined and autogenerated annotation rows for
4063 <li>Adjustment of alignment annotation pane height</li>
4064 <li>Annotation scrollbar for annotation panel</li>
4065 <li>Drag to reorder annotation rows in annotation panel</li>
4066 <li>'automaticScrolling' parameter</li>
4067 <li>Allow sequences with partial ID string matches to be
4068 annotated from GFF/Jalview features files</li>
4069 <li>Sequence logo annotation row in applet</li>
4070 <li>Absolute paths relative to host server in applet
4071 parameters are treated as such</li>
4072 <li>New in the JalviewLite javascript API:
4074 <li>JalviewLite.js javascript library</li>
4075 <li>Javascript callbacks for
4077 <li>Applet initialisation</li>
4078 <li>Sequence/alignment mouse-overs and selections</li>
4081 <li>scrollTo row and column alignment scrolling
4083 <li>Select sequence/alignment regions from javascript</li>
4084 <li>javascript structure viewer harness to pass
4085 messages between Jmol and Jalview when running as
4086 distinct applets</li>
4087 <li>sortBy method</li>
4088 <li>Set of applet and application examples shipped
4089 with documentation</li>
4090 <li>New example to demonstrate JalviewLite and Jmol
4091 javascript message exchange</li>
4093 </ul> <em>General</em>
4095 <li>Enable Jmol displays to be associated with multiple
4096 multiple alignments</li>
4097 <li>Option to automatically sort alignment with new tree</li>
4098 <li>User configurable link to enable redirects to a
4099 www.Jalview.org mirror</li>
4100 <li>Jmol colours option for Jmol displays</li>
4101 <li>Configurable newline string when writing alignment
4102 and other flat files</li>
4103 <li>Allow alignment annotation description lines to
4104 contain html tags</li>
4105 </ul> <em>Documentation and Development</em>
4107 <li>Add groovy test harness for bulk load testing to
4109 <li>Groovy script to load and align a set of sequences
4110 using a web service before displaying the result in the
4111 Jalview desktop</li>
4112 <li>Restructured javascript and applet api documentation</li>
4113 <li>Ant target to publish example html files with applet
4115 <li>Netbeans project for building Jalview from source</li>
4116 <li>ant task to create online javadoc for Jalview source</li>
4118 <td><em>Application</em>
4120 <li>User defined colourscheme throws exception when
4121 current built in colourscheme is saved as new scheme</li>
4122 <li>AlignFrame->Save in application pops up save
4123 dialog for valid filename/format</li>
4124 <li>Cannot view associated structure for UniProt sequence</li>
4125 <li>PDB file association breaks for UniProt sequence
4127 <li>Associate PDB from file dialog does not tell you
4128 which sequence is to be associated with the file</li>
4129 <li>Find All raises null pointer exception when query
4130 only matches sequence IDs</li>
4131 <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
4132 <li>Jalview project with Jmol views created with Jalview
4133 2.4 cannot be loaded</li>
4134 <li>Filetype associations not installed for webstart
4136 <li>Two or more chains in a single PDB file associated
4137 with sequences in different alignments do not get coloured
4138 by their associated sequence</li>
4139 <li>Visibility status of autocalculated annotation row
4140 not preserved when project is loaded</li>
4141 <li>Annotation row height and visibility attributes not
4142 stored in Jalview project</li>
4143 <li>Tree bootstraps are not preserved when saved as a
4144 Jalview project</li>
4145 <li>Envision2 workflow tooltips are corrupted</li>
4146 <li>Enabling show group conservation also enables colour
4147 by conservation</li>
4148 <li>Duplicate group associated conservation or consensus
4149 created on new view</li>
4150 <li>Annotation scrollbar not displayed after 'show
4151 all hidden annotation rows' option selected</li>
4152 <li>Alignment quality not updated after alignment
4153 annotation row is hidden then shown</li>
4154 <li>Preserve colouring of structures coloured by
4155 sequences in pre Jalview 2.7 projects</li>
4156 <li>Web service job parameter dialog is not laid out
4158 <li>Web services menu not refreshed after 'reset
4159 services' button is pressed in preferences</li>
4160 <li>Annotation off by one in Jalview v2_3 example project</li>
4161 <li>Structures imported from file and saved in project
4162 get name like jalview_pdb1234.txt when reloaded</li>
4163 <li>Jalview does not always retrieve progress of a JABAWS
4164 job execution in full once it is complete</li>
4165 </ul> <em>Applet</em>
4167 <li>Alignment height set incorrectly when lots of
4168 annotation rows are displayed</li>
4169 <li>Relative URLs in feature HTML text not resolved to
4171 <li>View follows highlighting does not work for positions
4173 <li><= shown as = in tooltip</li>
4174 <li>Export features raises exception when no features
4176 <li>Separator string used for serialising lists of IDs
4177 for javascript api is modified when separator string
4178 provided as parameter</li>
4179 <li>Null pointer exception when selecting tree leaves for
4180 alignment with no existing selection</li>
4181 <li>Relative URLs for datasources assumed to be relative
4182 to applet's codebase</li>
4183 <li>Status bar not updated after finished searching and
4184 search wraps around to first result</li>
4185 <li>StructureSelectionManager instance shared between
4186 several Jalview applets causes race conditions and memory
4188 <li>Hover tooltip and mouseover of position on structure
4189 not sent from Jmol in applet</li>
4190 <li>Certain sequences of javascript method calls to
4191 applet API fatally hang browser</li>
4192 </ul> <em>General</em>
4194 <li>View follows structure mouseover scrolls beyond
4195 position with wrapped view and hidden regions</li>
4196 <li>Find sequence position moves to wrong residue
4197 with/without hidden columns</li>
4198 <li>Sequence length given in alignment properties window
4200 <li>InvalidNumberFormat exceptions thrown when trying to
4201 import PDB like structure files</li>
4202 <li>Positional search results are only highlighted
4203 between user-supplied sequence start/end bounds</li>
4204 <li>End attribute of sequence is not validated</li>
4205 <li>Find dialog only finds first sequence containing a
4206 given sequence position</li>
4207 <li>Sequence numbering not preserved in MSF alignment
4209 <li>Jalview PDB file reader does not extract sequence
4210 from nucleotide chains correctly</li>
4211 <li>Structure colours not updated when tree partition
4212 changed in alignment</li>
4213 <li>Sequence associated secondary structure not correctly
4214 parsed in interleaved stockholm</li>
4215 <li>Colour by annotation dialog does not restore current
4217 <li>Hiding (nearly) all sequences doesn't work
4219 <li>Sequences containing lowercase letters are not
4220 properly associated with their pdb files</li>
4221 </ul> <em>Documentation and Development</em>
4223 <li>schemas/JalviewWsParamSet.xsd corrupted by
4224 ApplyCopyright tool</li>
4229 <div align="center">
4230 <strong><a name="Jalview2.6.1">2.6.1</a> </strong><br> <em>15/11/2010</em>
4233 <td><em>Application</em>
4235 <li>New warning dialog when the Jalview Desktop cannot
4236 contact web services</li>
4237 <li>JABA service parameters for a preset are shown in
4238 service job window</li>
4239 <li>JABA Service menu entries reworded</li>
4243 <li>Modeller PIR IO broken - cannot correctly import a
4244 pir file emitted by Jalview</li>
4245 <li>Existing feature settings transferred to new
4246 alignment view created from cut'n'paste</li>
4247 <li>Improved test for mixed amino/nucleotide chains when
4248 parsing PDB files</li>
4249 <li>Consensus and conservation annotation rows
4250 occasionally become blank for all new windows</li>
4251 <li>Exception raised when right clicking above sequences
4252 in wrapped view mode</li>
4253 </ul> <em>Application</em>
4255 <li>multiple multiply aligned structure views cause cpu
4256 usage to hit 100% and computer to hang</li>
4257 <li>Web Service parameter layout breaks for long user
4258 parameter names</li>
4259 <li>Jaba service discovery hangs desktop if Jaba server
4266 <div align="center">
4267 <strong><a name="Jalview2.6">2.6</a></strong><br> <em>26/9/2010</em>
4270 <td><em>Application</em>
4272 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
4273 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
4276 <li>Web Services preference tab</li>
4277 <li>Analysis parameters dialog box and user defined
4279 <li>Improved speed and layout of Envision2 service menu</li>
4280 <li>Superpose structures using associated sequence
4282 <li>Export coordinates and projection as CSV from PCA
4284 </ul> <em>Applet</em>
4286 <li>enable javascript: execution by the applet via the
4287 link out mechanism</li>
4288 </ul> <em>Other</em>
4290 <li>Updated the Jmol Jalview interface to work with Jmol
4292 <li>The Jalview Desktop and JalviewLite applet now
4293 require Java 1.5</li>
4294 <li>Allow Jalview feature colour specification for GFF
4295 sequence annotation files</li>
4296 <li>New 'colour by label' keword in Jalview feature file
4297 type colour specification</li>
4298 <li>New Jalview Desktop Groovy API method that allows a
4299 script to check if it being run in an interactive session or
4300 in a batch operation from the Jalview command line</li>
4304 <li>clustalx colourscheme colours Ds preferentially when
4305 both D+E are present in over 50% of the column</li>
4306 </ul> <em>Application</em>
4308 <li>typo in AlignmentFrame->View->Hide->all but
4309 selected Regions menu item</li>
4310 <li>sequence fetcher replaces ',' for ';' when the ',' is
4311 part of a valid accession ID</li>
4312 <li>fatal OOM if object retrieved by sequence fetcher
4313 runs out of memory</li>
4314 <li>unhandled Out of Memory Error when viewing pca
4315 analysis results</li>
4316 <li>InstallAnywhere builds fail to launch on OS X java
4317 10.5 update 4 (due to apple Java 1.6 update)</li>
4318 <li>Installanywhere Jalview silently fails to launch</li>
4319 </ul> <em>Applet</em>
4321 <li>Jalview.getFeatureGroups() raises an
4322 ArrayIndexOutOfBoundsException if no feature groups are
4329 <div align="center">
4330 <strong><a name="Jalview2.5.1">2.5.1</a></strong><br> <em>14/6/2010</em>
4336 <li>Alignment prettyprinter doesn't cope with long
4338 <li>clustalx colourscheme colours Ds preferentially when
4339 both D+E are present in over 50% of the column</li>
4340 <li>nucleic acid structures retrieved from PDB do not
4341 import correctly</li>
4342 <li>More columns get selected than were clicked on when a
4343 number of columns are hidden</li>
4344 <li>annotation label popup menu not providing correct
4345 add/hide/show options when rows are hidden or none are
4347 <li>Stockholm format shown in list of readable formats,
4348 and parser copes better with alignments from RFAM.</li>
4349 <li>CSV output of consensus only includes the percentage
4350 of all symbols if sequence logo display is enabled</li>
4352 </ul> <em>Applet</em>
4354 <li>annotation panel disappears when annotation is
4356 </ul> <em>Application</em>
4358 <li>Alignment view not redrawn properly when new
4359 alignment opened where annotation panel is visible but no
4360 annotations are present on alignment</li>
4361 <li>pasted region containing hidden columns is
4362 incorrectly displayed in new alignment window</li>
4363 <li>Jalview slow to complete operations when stdout is
4364 flooded (fix is to close the Jalview console)</li>
4365 <li>typo in AlignmentFrame->View->Hide->all but
4366 selected Rregions menu item.</li>
4367 <li>inconsistent group submenu and Format submenu entry
4368 'Un' or 'Non'conserved</li>
4369 <li>Sequence feature settings are being shared by
4370 multiple distinct alignments</li>
4371 <li>group annotation not recreated when tree partition is
4373 <li>double click on group annotation to select sequences
4374 does not propagate to associated trees</li>
4375 <li>Mac OSX specific issues:
4377 <li>exception raised when mouse clicked on desktop
4378 window background</li>
4379 <li>Desktop menu placed on menu bar and application
4380 name set correctly</li>
4381 <li>sequence feature settings not wide enough for the
4382 save feature colourscheme button</li>
4391 <div align="center">
4392 <strong><a name="Jalview2.5">2.5</a></strong><br> <em>30/4/2010</em>
4395 <td><em>New Capabilities</em>
4397 <li>URL links generated from description line for
4398 regular-expression based URL links (applet and application)
4400 <li>Non-positional feature URL links are shown in link
4402 <li>Linked viewing of nucleic acid sequences and
4404 <li>Automatic Scrolling option in View menu to display
4405 the currently highlighted region of an alignment.</li>
4406 <li>Order an alignment by sequence length, or using the
4407 average score or total feature count for each sequence.</li>
4408 <li>Shading features by score or associated description</li>
4409 <li>Subdivide alignment and groups based on identity of
4410 selected subsequence (Make Groups from Selection).</li>
4411 <li>New hide/show options including Shift+Control+H to
4412 hide everything but the currently selected region.</li>
4413 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
4414 </ul> <em>Application</em>
4416 <li>Fetch DB References capabilities and UI expanded to
4417 support retrieval from DAS sequence sources</li>
4418 <li>Local DAS Sequence sources can be added via the
4419 command line or via the Add local source dialog box.</li>
4420 <li>DAS Dbref and DbxRef feature types are parsed as
4421 database references and protein_name is parsed as
4422 description line (BioSapiens terms).</li>
4423 <li>Enable or disable non-positional feature and database
4424 references in sequence ID tooltip from View menu in
4426 <!-- <li>New hidden columns and rows and representatives capabilities
4427 in annotations file (in progress - not yet fully implemented)</li> -->
4428 <li>Group-associated consensus, sequence logos and
4429 conservation plots</li>
4430 <li>Symbol distributions for each column can be exported
4431 and visualized as sequence logos</li>
4432 <li>Optionally scale multi-character column labels to fit
4433 within each column of annotation row<!-- todo for applet -->
4435 <li>Optional automatic sort of associated alignment view
4436 when a new tree is opened.</li>
4437 <li>Jalview Java Console</li>
4438 <li>Better placement of desktop window when moving
4439 between different screens.</li>
4440 <li>New preference items for sequence ID tooltip and
4441 consensus annotation</li>
4442 <li>Client to submit sequences and IDs to Envision2
4444 <li><em>Vamsas Capabilities</em>
4446 <li>Improved VAMSAS synchronization (Jalview archive
4447 used to preserve views, structures, and tree display
4449 <li>Import of vamsas documents from disk or URL via
4451 <li>Sharing of selected regions between views and
4452 with other VAMSAS applications (Experimental feature!)</li>
4453 <li>Updated API to VAMSAS version 0.2</li>
4455 </ul> <em>Applet</em>
4457 <li>Middle button resizes annotation row height</li>
4460 <li>sortByTree (true/false) - automatically sort the
4461 associated alignment view by the tree when a new tree is
4463 <li>showTreeBootstraps (true/false) - show or hide
4464 branch bootstraps (default is to show them if available)</li>
4465 <li>showTreeDistances (true/false) - show or hide
4466 branch lengths (default is to show them if available)</li>
4467 <li>showUnlinkedTreeNodes (true/false) - indicate if
4468 unassociated nodes should be highlighted in the tree
4470 <li>heightScale and widthScale (1.0 or more) -
4471 increase the height or width of a cell in the alignment
4472 grid relative to the current font size.</li>
4475 <li>Non-positional features displayed in sequence ID
4477 </ul> <em>Other</em>
4479 <li>Features format: graduated colour definitions and
4480 specification of feature scores</li>
4481 <li>Alignment Annotations format: new keywords for group
4482 associated annotation (GROUP_REF) and annotation row display
4483 properties (ROW_PROPERTIES)</li>
4484 <li>XML formats extended to support graduated feature
4485 colourschemes, group associated annotation, and profile
4486 visualization settings.</li></td>
4489 <li>Source field in GFF files parsed as feature source
4490 rather than description</li>
4491 <li>Non-positional features are now included in sequence
4492 feature and gff files (controlled via non-positional feature
4493 visibility in tooltip).</li>
4494 <li>URL links generated for all feature links (bugfix)</li>
4495 <li>Added URL embedding instructions to features file
4497 <li>Codons containing ambiguous nucleotides translated as
4498 'X' in peptide product</li>
4499 <li>Match case switch in find dialog box works for both
4500 sequence ID and sequence string and query strings do not
4501 have to be in upper case to match case-insensitively.</li>
4502 <li>AMSA files only contain first column of
4503 multi-character column annotation labels</li>
4504 <li>Jalview Annotation File generation/parsing consistent
4505 with documentation (e.g. Stockholm annotation can be
4506 exported and re-imported)</li>
4507 <li>PDB files without embedded PDB IDs given a friendly
4509 <li>Find incrementally searches ID string matches as well
4510 as subsequence matches, and correctly reports total number
4514 <li>Better handling of exceptions during sequence
4516 <li>Dasobert generated non-positional feature URL
4517 link text excludes the start_end suffix</li>
4518 <li>DAS feature and source retrieval buttons disabled
4519 when fetch or registry operations in progress.</li>
4520 <li>PDB files retrieved from URLs are cached properly</li>
4521 <li>Sequence description lines properly shared via
4523 <li>Sequence fetcher fetches multiple records for all
4525 <li>Ensured that command line das feature retrieval
4526 completes before alignment figures are generated.</li>
4527 <li>Reduced time taken when opening file browser for
4529 <li>isAligned check prior to calculating tree, PCA or
4530 submitting an MSA to JNet now excludes hidden sequences.</li>
4531 <li>User defined group colours properly recovered
4532 from Jalview projects.</li>
4541 <div align="center">
4542 <strong>2.4.0.b2</strong><br> 28/10/2009
4547 <li>Experimental support for google analytics usage
4549 <li>Jalview privacy settings (user preferences and docs).</li>
4554 <li>Race condition in applet preventing startup in
4556 <li>Exception when feature created from selection beyond
4557 length of sequence.</li>
4558 <li>Allow synthetic PDB files to be imported gracefully</li>
4559 <li>Sequence associated annotation rows associate with
4560 all sequences with a given id</li>
4561 <li>Find function matches case-insensitively for sequence
4562 ID string searches</li>
4563 <li>Non-standard characters do not cause pairwise
4564 alignment to fail with exception</li>
4565 </ul> <em>Application Issues</em>
4567 <li>Sequences are now validated against EMBL database</li>
4568 <li>Sequence fetcher fetches multiple records for all
4570 </ul> <em>InstallAnywhere Issues</em>
4572 <li>Dock icon works for Mac OS X java (Mac 1.6 update
4573 issue with installAnywhere mechanism)</li>
4574 <li>Command line launching of JARs from InstallAnywhere
4575 version (java class versioning error fixed)</li>
4582 <div align="center">
4583 <strong>2.4</strong><br> 27/8/2008
4586 <td><em>User Interface</em>
4588 <li>Linked highlighting of codon and amino acid from
4589 translation and protein products</li>
4590 <li>Linked highlighting of structure associated with
4591 residue mapping to codon position</li>
4592 <li>Sequence Fetcher provides example accession numbers
4593 and 'clear' button</li>
4594 <li>MemoryMonitor added as an option under Desktop's
4596 <li>Extract score function to parse whitespace separated
4597 numeric data in description line</li>
4598 <li>Column labels in alignment annotation can be centred.</li>
4599 <li>Tooltip for sequence associated annotation give name
4601 </ul> <em>Web Services and URL fetching</em>
4603 <li>JPred3 web service</li>
4604 <li>Prototype sequence search client (no public services
4606 <li>Fetch either seed alignment or full alignment from
4608 <li>URL Links created for matching database cross
4609 references as well as sequence ID</li>
4610 <li>URL Links can be created using regular-expressions</li>
4611 </ul> <em>Sequence Database Connectivity</em>
4613 <li>Retrieval of cross-referenced sequences from other
4615 <li>Generalised database reference retrieval and
4616 validation to all fetchable databases</li>
4617 <li>Fetch sequences from DAS sources supporting the
4618 sequence command</li>
4619 </ul> <em>Import and Export</em>
4620 <li>export annotation rows as CSV for spreadsheet import</li>
4621 <li>Jalview projects record alignment dataset associations,
4622 EMBL products, and cDNA sequence mappings</li>
4623 <li>Sequence Group colour can be specified in Annotation
4625 <li>Ad-hoc colouring of group in Annotation File using RGB
4626 triplet as name of colourscheme</li>
4627 </ul> <em>VAMSAS Client capabilities (Experimental)</em>
4629 <li>treenode binding for VAMSAS tree exchange</li>
4630 <li>local editing and update of sequences in VAMSAS
4631 alignments (experimental)</li>
4632 <li>Create new or select existing session to join</li>
4633 <li>load and save of vamsas documents</li>
4634 </ul> <em>Application command line</em>
4636 <li>-tree parameter to open trees (introduced for passing
4638 <li>-fetchfrom command line argument to specify nicknames
4639 of DAS servers to query for alignment features</li>
4640 <li>-dasserver command line argument to add new servers
4641 that are also automatically queried for features</li>
4642 <li>-groovy command line argument executes a given groovy
4643 script after all input data has been loaded and parsed</li>
4644 </ul> <em>Applet-Application data exchange</em>
4646 <li>Trees passed as applet parameters can be passed to
4647 application (when using "View in full
4648 application")</li>
4649 </ul> <em>Applet Parameters</em>
4651 <li>feature group display control parameter</li>
4652 <li>debug parameter</li>
4653 <li>showbutton parameter</li>
4654 </ul> <em>Applet API methods</em>
4656 <li>newView public method</li>
4657 <li>Window (current view) specific get/set public methods</li>
4658 <li>Feature display control methods</li>
4659 <li>get list of currently selected sequences</li>
4660 </ul> <em>New Jalview distribution features</em>
4662 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
4663 <li>RELEASE file gives build properties for the latest
4664 Jalview release.</li>
4665 <li>Java 1.1 Applet build made easier and donotobfuscate
4666 property controls execution of obfuscator</li>
4667 <li>Build target for generating source distribution</li>
4668 <li>Debug flag for javacc</li>
4669 <li>.jalview_properties file is documented (slightly) in
4670 jalview.bin.Cache</li>
4671 <li>Continuous Build Integration for stable and
4672 development version of Application, Applet and source
4677 <li>selected region output includes visible annotations
4678 (for certain formats)</li>
4679 <li>edit label/displaychar contains existing label/char
4681 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
4682 <li>shorter peptide product names from EMBL records</li>
4683 <li>Newick string generator makes compact representations</li>
4684 <li>bootstrap values parsed correctly for tree files with
4686 <li>pathological filechooser bug avoided by not allowing
4687 filenames containing a ':'</li>
4688 <li>Fixed exception when parsing GFF files containing
4689 global sequence features</li>
4690 <li>Alignment datasets are finalized only when number of
4691 references from alignment sequences goes to zero</li>
4692 <li>Close of tree branch colour box without colour
4693 selection causes cascading exceptions</li>
4694 <li>occasional negative imgwidth exceptions</li>
4695 <li>better reporting of non-fatal warnings to user when
4696 file parsing fails.</li>
4697 <li>Save works when Jalview project is default format</li>
4698 <li>Save as dialog opened if current alignment format is
4699 not a valid output format</li>
4700 <li>UniProt canonical names introduced for both das and
4702 <li>Histidine should be midblue (not pink!) in Zappo</li>
4703 <li>error messages passed up and output when data read
4705 <li>edit undo recovers previous dataset sequence when
4706 sequence is edited</li>
4707 <li>allow PDB files without pdb ID HEADER lines (like
4708 those generated by MODELLER) to be read in properly</li>
4709 <li>allow reading of JPred concise files as a normal
4711 <li>Stockholm annotation parsing and alignment properties
4712 import fixed for PFAM records</li>
4713 <li>Structure view windows have correct name in Desktop
4715 <li>annotation consisting of sequence associated scores
4716 can be read and written correctly to annotation file</li>
4717 <li>Aligned cDNA translation to aligned peptide works
4719 <li>Fixed display of hidden sequence markers and
4720 non-italic font for representatives in Applet</li>
4721 <li>Applet Menus are always embedded in applet window on
4723 <li>Newly shown features appear at top of stack (in
4725 <li>Annotations added via parameter not drawn properly
4726 due to null pointer exceptions</li>
4727 <li>Secondary structure lines are drawn starting from
4728 first column of alignment</li>
4729 <li>UniProt XML import updated for new schema release in
4731 <li>Sequence feature to sequence ID match for Features
4732 file is case-insensitive</li>
4733 <li>Sequence features read from Features file appended to
4734 all sequences with matching IDs</li>
4735 <li>PDB structure coloured correctly for associated views
4736 containing a sub-sequence</li>
4737 <li>PDB files can be retrieved by applet from Jar files</li>
4738 <li>feature and annotation file applet parameters
4739 referring to different directories are retrieved correctly</li>
4740 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
4741 <li>Fixed application hang whilst waiting for
4742 splash-screen version check to complete</li>
4743 <li>Applet properly URLencodes input parameter values
4744 when passing them to the launchApp service</li>
4745 <li>display name and local features preserved in results
4746 retrieved from web service</li>
4747 <li>Visual delay indication for sequence retrieval and
4748 sequence fetcher initialisation</li>
4749 <li>updated Application to use DAS 1.53e version of
4750 dasobert DAS client</li>
4751 <li>Re-instated Full AMSA support and .amsa file
4753 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
4761 <div align="center">
4762 <strong>2.3</strong><br> 9/5/07
4767 <li>Jmol 11.0.2 integration</li>
4768 <li>PDB views stored in Jalview XML files</li>
4769 <li>Slide sequences</li>
4770 <li>Edit sequence in place</li>
4771 <li>EMBL CDS features</li>
4772 <li>DAS Feature mapping</li>
4773 <li>Feature ordering</li>
4774 <li>Alignment Properties</li>
4775 <li>Annotation Scores</li>
4776 <li>Sort by scores</li>
4777 <li>Feature/annotation editing in applet</li>
4782 <li>Headless state operation in 2.2.1</li>
4783 <li>Incorrect and unstable DNA pairwise alignment</li>
4784 <li>Cut and paste of sequences with annotation</li>
4785 <li>Feature group display state in XML</li>
4786 <li>Feature ordering in XML</li>
4787 <li>blc file iteration selection using filename # suffix</li>
4788 <li>Stockholm alignment properties</li>
4789 <li>Stockhom alignment secondary structure annotation</li>
4790 <li>2.2.1 applet had no feature transparency</li>
4791 <li>Number pad keys can be used in cursor mode</li>
4792 <li>Structure Viewer mirror image resolved</li>
4799 <div align="center">
4800 <strong>2.2.1</strong><br> 12/2/07
4805 <li>Non standard characters can be read and displayed
4806 <li>Annotations/Features can be imported/exported to the
4808 <li>Applet allows editing of sequence/annotation/group
4809 name & description
4810 <li>Preference setting to display sequence name in
4812 <li>Annotation file format extended to allow
4813 Sequence_groups to be defined
4814 <li>Default opening of alignment overview panel can be
4815 specified in preferences
4816 <li>PDB residue numbering annotation added to associated
4822 <li>Applet crash under certain Linux OS with Java 1.6
4824 <li>Annotation file export / import bugs fixed
4825 <li>PNG / EPS image output bugs fixed
4831 <div align="center">
4832 <strong>2.2</strong><br> 27/11/06
4837 <li>Multiple views on alignment
4838 <li>Sequence feature editing
4839 <li>"Reload" alignment
4840 <li>"Save" to current filename
4841 <li>Background dependent text colour
4842 <li>Right align sequence ids
4843 <li>User-defined lower case residue colours
4846 <li>Menu item accelerator keys
4847 <li>Control-V pastes to current alignment
4848 <li>Cancel button for DAS Feature Fetching
4849 <li>PCA and PDB Viewers zoom via mouse roller
4850 <li>User-defined sub-tree colours and sub-tree selection
4852 <li>'New Window' button on the 'Output to Text box'
4857 <li>New memory efficient Undo/Redo System
4858 <li>Optimised symbol lookups and conservation/consensus
4860 <li>Region Conservation/Consensus recalculated after
4862 <li>Fixed Remove Empty Columns Bug (empty columns at end
4864 <li>Slowed DAS Feature Fetching for increased robustness.
4866 <li>Made angle brackets in ASCII feature descriptions
4868 <li>Re-instated Zoom function for PCA
4869 <li>Sequence descriptions conserved in web service
4871 <li>UniProt ID discoverer uses any word separated by
4873 <li>WsDbFetch query/result association resolved
4874 <li>Tree leaf to sequence mapping improved
4875 <li>Smooth fonts switch moved to FontChooser dialog box.
4882 <div align="center">
4883 <strong>2.1.1</strong><br> 12/9/06
4888 <li>Copy consensus sequence to clipboard</li>
4893 <li>Image output - rightmost residues are rendered if
4894 sequence id panel has been resized</li>
4895 <li>Image output - all offscreen group boundaries are
4897 <li>Annotation files with sequence references - all
4898 elements in file are relative to sequence position</li>
4899 <li>Mac Applet users can use Alt key for group editing</li>
4905 <div align="center">
4906 <strong>2.1</strong><br> 22/8/06
4911 <li>MAFFT Multiple Alignment in default Web Service list</li>
4912 <li>DAS Feature fetching</li>
4913 <li>Hide sequences and columns</li>
4914 <li>Export Annotations and Features</li>
4915 <li>GFF file reading / writing</li>
4916 <li>Associate structures with sequences from local PDB
4918 <li>Add sequences to exisiting alignment</li>
4919 <li>Recently opened files / URL lists</li>
4920 <li>Applet can launch the full application</li>
4921 <li>Applet has transparency for features (Java 1.2
4923 <li>Applet has user defined colours parameter</li>
4924 <li>Applet can load sequences from parameter
4925 "sequence<em>x</em>"
4931 <li>Redundancy Panel reinstalled in the Applet</li>
4932 <li>Monospaced font - EPS / rescaling bug fixed</li>
4933 <li>Annotation files with sequence references bug fixed</li>
4939 <div align="center">
4940 <strong>2.08.1</strong><br> 2/5/06
4945 <li>Change case of selected region from Popup menu</li>
4946 <li>Choose to match case when searching</li>
4947 <li>Middle mouse button and mouse movement can compress /
4948 expand the visible width and height of the alignment</li>
4953 <li>Annotation Panel displays complete JNet results</li>
4959 <div align="center">
4960 <strong>2.08b</strong><br> 18/4/06
4966 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
4967 <li>Righthand label on wrapped alignments shows correct
4974 <div align="center">
4975 <strong>2.08</strong><br> 10/4/06
4980 <li>Editing can be locked to the selection area</li>
4981 <li>Keyboard editing</li>
4982 <li>Create sequence features from searches</li>
4983 <li>Precalculated annotations can be loaded onto
4985 <li>Features file allows grouping of features</li>
4986 <li>Annotation Colouring scheme added</li>
4987 <li>Smooth fonts off by default - Faster rendering</li>
4988 <li>Choose to toggle Autocalculate Consensus On/Off</li>
4993 <li>Drag & Drop fixed on Linux</li>
4994 <li>Jalview Archive file faster to load/save, sequence
4995 descriptions saved.</li>
5001 <div align="center">
5002 <strong>2.07</strong><br> 12/12/05
5007 <li>PDB Structure Viewer enhanced</li>
5008 <li>Sequence Feature retrieval and display enhanced</li>
5009 <li>Choose to output sequence start-end after sequence
5010 name for file output</li>
5011 <li>Sequence Fetcher WSDBFetch@EBI</li>
5012 <li>Applet can read feature files, PDB files and can be
5013 used for HTML form input</li>
5018 <li>HTML output writes groups and features</li>
5019 <li>Group editing is Control and mouse click</li>
5020 <li>File IO bugs</li>
5026 <div align="center">
5027 <strong>2.06</strong><br> 28/9/05
5032 <li>View annotations in wrapped mode</li>
5033 <li>More options for PCA viewer</li>
5038 <li>GUI bugs resolved</li>
5039 <li>Runs with -nodisplay from command line</li>
5045 <div align="center">
5046 <strong>2.05b</strong><br> 15/9/05
5051 <li>Choose EPS export as lineart or text</li>
5052 <li>Jar files are executable</li>
5053 <li>Can read in Uracil - maps to unknown residue</li>
5058 <li>Known OutOfMemory errors give warning message</li>
5059 <li>Overview window calculated more efficiently</li>
5060 <li>Several GUI bugs resolved</li>
5066 <div align="center">
5067 <strong>2.05</strong><br> 30/8/05
5072 <li>Edit and annotate in "Wrapped" view</li>
5077 <li>Several GUI bugs resolved</li>
5083 <div align="center">
5084 <strong>2.04</strong><br> 24/8/05
5089 <li>Hold down mouse wheel & scroll to change font
5095 <li>Improved JPred client reliability</li>
5096 <li>Improved loading of Jalview files</li>
5102 <div align="center">
5103 <strong>2.03</strong><br> 18/8/05
5108 <li>Set Proxy server name and port in preferences</li>
5109 <li>Multiple URL links from sequence ids</li>
5110 <li>User Defined Colours can have a scheme name and added
5112 <li>Choose to ignore gaps in consensus calculation</li>
5113 <li>Unix users can set default web browser</li>
5114 <li>Runs without GUI for batch processing</li>
5115 <li>Dynamically generated Web Service Menus</li>
5120 <li>InstallAnywhere download for Sparc Solaris</li>
5126 <div align="center">
5127 <strong>2.02</strong><br> 18/7/05
5133 <li>Copy & Paste order of sequences maintains
5134 alignment order.</li>
5140 <div align="center">
5141 <strong>2.01</strong><br> 12/7/05
5146 <li>Use delete key for deleting selection.</li>
5147 <li>Use Mouse wheel to scroll sequences.</li>
5148 <li>Help file updated to describe how to add alignment
5150 <li>Version and build date written to build properties
5152 <li>InstallAnywhere installation will check for updates
5153 at launch of Jalview.</li>
5158 <li>Delete gaps bug fixed.</li>
5159 <li>FileChooser sorts columns.</li>
5160 <li>Can remove groups one by one.</li>
5161 <li>Filechooser icons installed.</li>
5162 <li>Finder ignores return character when searching.
5163 Return key will initiate a search.<br>
5170 <div align="center">
5171 <strong>2.0</strong><br> 20/6/05
5176 <li>New codebase</li>