3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6.1)
4 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Release History</title>
23 <p><strong>Release History</strong></p>
26 <td width="60" nowrap>
27 <div align="center"><em><strong>Release</strong></em></div>
30 <div align="center"><em><strong>New Features</strong></em></div>
33 <div align="center"><em><strong>Issues Resolved</strong></em></div>
38 <div align="center"><strong><a name="Jalview2.6.1">2.6.1</a></strong><br>
39 <em>15/11/2010</em></div>
41 <td><em>Application</em>
43 <li>New warning dialog when the Jalview Desktop cannot contact web services</li>
44 <li>JABA service parameters for a preset are shown in service job window</li>
45 <li>JABA Service menu entries reworded</li>
50 <li>Modeller PIR IO broken - cannot correctly import a pir file emitted by jalview</li>
51 <li>Existing feature settings transferred to new alignment view created from cut'n'paste</li>
52 <li>Improved test for mixed amino/nucleotide chains when parsing PDB files</li>
53 <li>Consensus and conservation annotation rows occasionally become blank for all new windows</li>
54 <li>Exception raised when right clicking above sequences in wrapped view mode</li>
58 <li>multiple multiply aligned structure views cause cpu usage to hit 100% and computer to hang</li>
59 <li>Web Service parameter layout breaks for long user parameter names</li>
60 <li>Jaba service discovery hangs desktop if Jaba server is down</li>
66 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
67 <em>26/9/2010</em></div>
69 <td><em>Application</em>
71 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
72 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
73 <li>Web Services preference tab</li>
74 <li>Analysis parameters dialog box and user defined preferences</li>
75 <li>Improved speed and layout of Envision2 service menu</li>
76 <li>Superpose structures using associated sequence alignment</li>
77 <li>Export coordinates and projection as CSV from PCA viewer</li>
81 <li>enable javascript: execution by the applet via the link out
86 <li>Updated the Jmol Jalview interface to work with Jmol series
88 <li>The Jalview Desktop and JalviewLite applet now require Java
90 <li>Allow Jalview feature colour specification for GFF sequence
92 <li>New 'colour by label' keword in jalview feature file type
93 colour specification</li>
94 <li>New Jalview Desktop Groovy API method that allows a script
95 to check if it being run in an interactive session or in a batch
96 operation from the jalview command line</li>
101 <li>clustalx colourscheme colours Ds preferentially when both
102 D+E are present in over 50% of the column</li>
107 <li>typo in AlignmentFrame->View->Hide->all but
108 selected Regions menu item</li>
109 <li>sequence fetcher replaces ',' for ';' when the ',' is part
110 of a valid accession ID</li>
111 <li>fatal OOM if object retrieved by sequence fetcher runs out
113 <li>unhandled Out of Memory Error when viewing pca analysis
115 <li>InstallAnywhere builds fail to launch on OS X java 10.5
116 update 4 (due to apple Java 1.6 update)</li>
117 <li>Installanywhere Jalview silently fails to launch</li>
121 <li>Jalview.getFeatureGroups() raises an
122 ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
128 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
129 <em>14/6/2010</em></div>
134 <li>Alignment prettyprinter doesn't cope with long sequence IDs
136 <li>clustalx colourscheme colours Ds preferentially when both
137 D+E are present in over 50% of the column</li>
138 <li>nucleic acid structures retrieved from PDB do not import
140 <li>More columns get selected than were clicked on when a number
141 of columns are hidden</li>
142 <li>annotation label popup menu not providing correct
143 add/hide/show options when rows are hidden or none are present</li>
144 <li>Stockholm format shown in list of readable formats, and
145 parser copes better with alignments from RFAM.</li>
146 <li>CSV output of consensus only includes the percentage of all
147 symbols if sequence logo display is enabled</li>
152 <li>annotation panel disappears when annotation is
157 <li>Alignment view not redrawn properly when new alignment
158 opened where annotation panel is visible but no annotations are
159 present on alignment</li>
160 <li>pasted region containing hidden columns is incorrectly
161 displayed in new alignment window</li>
162 <li>Jalview slow to complete operations when stdout is flooded
163 (fix is to close the Jalview console)</li>
164 <li>typo in AlignmentFrame->View->Hide->all but
165 selected Rregions menu item.</li>
166 <li>inconsistent group submenu and Format submenu entry 'Un' or
168 <li>Sequence feature settings are being shared by multiple
169 distinct alignments</li>
170 <li>group annotation not recreated when tree partition is
172 <li>double click on group annotation to select sequences does
173 not propagate to associated trees</li>
174 <li>Mac OSX specific issues:
176 <li>exception raised when mouse clicked on desktop window
178 <li>Desktop menu placed on menu bar and application name set
180 <li>sequence feature settings not wide enough for the save
181 feature colourscheme button</li>
190 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
191 <em>30/4/2010</em></div>
193 <td><em>New Capabilities</em>
195 <li>URL links generated from description line for
196 regular-expression based URL links (applet and application)
197 <li>Non-positional feature URL links are shown in link menu</li>
198 <li>Linked viewing of nucleic acid sequences and structures</li>
199 <li>Automatic Scrolling option in View menu to display the
200 currently highlighted region of an alignment.</li>
201 <li>Order an alignment by sequence length, or using the average
202 score or total feature count for each sequence.</li>
203 <li>Shading features by score or associated description</li>
204 <li>Subdivide alignment and groups based on identity of selected
205 subsequence (Make Groups from Selection).</li>
206 <li>New hide/show options including Shift+Control+H to hide
207 everything but the currently selected region.</li>
208 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
212 <li>Fetch DB References capabilities and UI expanded to support
213 retrieval from DAS sequence sources</li>
214 <li>Local DAS Sequence sources can be added via the command line
215 or via the Add local source dialog box.</li>
216 <li>DAS Dbref and DbxRef feature types are parsed as database
217 references and protein_name is parsed as description line (BioSapiens
219 <li>Enable or disable non-positional feature and database
220 references in sequence ID tooltip from View menu in application.</li>
221 <!-- <li>New hidden columns and rows and representatives capabilities
222 in annotations file (in progress - not yet fully implemented)</li> -->
223 <li>Group-associated consensus, sequence logos and conservation
225 <li>Symbol distributions for each column can be exported and
226 visualized as sequence logos</li>
227 <li>Optionally scale multi-character column labels to fit within
228 each column of annotation row<!-- todo for applet --></li>
229 <li>Optional automatic sort of associated alignment view when a
230 new tree is opened.</li>
231 <li>Jalview Java Console</li>
232 <li>Better placement of desktop window when moving between
233 different screens.</li>
234 <li>New preference items for sequence ID tooltip and consensus
236 <li>Client to submit sequences and IDs to <a
237 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
238 <li><em>Vamsas Capabilities</em>
240 <li>Improved VAMSAS synchronization (jalview archive used to
241 preserve views, structures, and tree display settings)</li>
242 <li>Import of vamsas documents from disk or URL via command
244 <li>Sharing of selected regions between views and with other
245 VAMSAS applications (Experimental feature!)</li>
246 <li>Updated API to VAMSAS version 0.2</li>
252 <li>Middle button resizes annotation row height</li>
255 <li>sortByTree (true/false) - automatically sort the associated
256 alignment view by the tree when a new tree is opened.</li>
257 <li>showTreeBootstraps (true/false) - show or hide branch
258 bootstraps (default is to show them if available)</li>
259 <li>showTreeDistances (true/false) - show or hide branch
260 lengths (default is to show them if available)</li>
261 <li>showUnlinkedTreeNodes (true/false) - indicate if
262 unassociated nodes should be highlighted in the tree view</li>
263 <li>heightScale and widthScale (1.0 or more) - increase the
264 height or width of a cell in the alignment grid relative to the
265 current font size.</li>
268 <li>Non-positional features displayed in sequence ID tooltip</li>
272 <li>Features format: graduated colour definitions and
273 specification of feature scores</li>
274 <li>Alignment Annotations format: new keywords for group
275 associated annotation (GROUP_REF) and annotation row display
276 properties (ROW_PROPERTIES)</li>
277 <li>XML formats extended to support graduated feature
278 colourschemes, group associated annotation, and profile visualization
283 <li>Source field in GFF files parsed as feature source rather
284 than description</li>
285 <li>Non-positional features are now included in sequence feature
286 and gff files (controlled via non-positional feature visibility in
288 <li>URL links generated for all feature links (bugfix)</li>
289 <li>Added URL embedding instructions to features file
291 <li>Codons containing ambiguous nucleotides translated as 'X' in
293 <li>Match case switch in find dialog box works for both sequence
294 ID and sequence string and query strings do not have to be in upper
295 case to match case-insensitively.</li>
296 <li>AMSA files only contain first column of multi-character
297 column annotation labels</li>
298 <li>Jalview Annotation File generation/parsing consistent with
299 documentation (e.g. Stockholm annotation can be exported and
301 <li>PDB files without embedded PDB IDs given a friendly name</li>
302 <li>Find incrementally searches ID string matches as well as
303 subsequence matches, and correctly reports total number of both.</li>
306 <li>Better handling of exceptions during sequence retrieval</li>
307 <li>Dasobert generated non-positional feature URL link text
308 excludes the start_end suffix</li>
309 <li>DAS feature and source retrieval buttons disabled when
310 fetch or registry operations in progress.</li>
311 <li>PDB files retrieved from URLs are cached properly</li>
312 <li>Sequence description lines properly shared via VAMSAS</li>
313 <li>Sequence fetcher fetches multiple records for all data
315 <li>Ensured that command line das feature retrieval completes
316 before alignment figures are generated.</li>
317 <li>Reduced time taken when opening file browser for first
319 <li>isAligned check prior to calculating tree, PCA or
320 submitting an MSA to JNet now excludes hidden sequences.</li>
321 <li>User defined group colours properly recovered from Jalview
331 <div align="center"><strong>2.4.0.b2</strong><br>
336 <li>Experimental support for google analytics usage tracking.</li>
337 <li>Jalview privacy settings (user preferences and docs).</li>
342 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
343 <li>Exception when feature created from selection beyond length
345 <li>Allow synthetic PDB files to be imported gracefully</li>
346 <li>Sequence associated annotation rows associate with all
347 sequences with a given id</li>
348 <li>Find function matches case-insensitively for sequence ID
350 <li>Non-standard characters do not cause pairwise alignment to
351 fail with exception</li>
353 <em>Application Issues</em>
355 <li>Sequences are now validated against EMBL database</li>
356 <li>Sequence fetcher fetches multiple records for all data
359 <em>InstallAnywhere Issues</em>
361 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
362 installAnywhere mechanism)</li>
363 <li>Command line launching of JARs from InstallAnywhere version
364 (java class versioning error fixed)</li>
371 <div align="center"><strong>2.4</strong><br>
374 <td><em>User Interface</em>
376 <li>Linked highlighting of codon and amino acid from translation
377 and protein products</li>
378 <li>Linked highlighting of structure associated with residue
379 mapping to codon position</li>
380 <li>Sequence Fetcher provides example accession numbers and
382 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
383 <li>Extract score function to parse whitespace separated numeric
384 data in description line</li>
385 <li>Column labels in alignment annotation can be centred.</li>
386 <li>Tooltip for sequence associated annotation give name of
389 <em>Web Services and URL fetching</em>
391 <li>JPred3 web service</li>
392 <li>Prototype sequence search client (no public services
394 <li>Fetch either seed alignment or full alignment from PFAM</li>
395 <li>URL Links created for matching database cross references as
396 well as sequence ID</li>
397 <li>URL Links can be created using regular-expressions</li>
399 <em>Sequence Database Connectivity</em>
401 <li>Retrieval of cross-referenced sequences from other databases
403 <li>Generalised database reference retrieval and validation to
404 all fetchable databases</li>
405 <li>Fetch sequences from DAS sources supporting the sequence
408 <em>Import and Export</em>
409 <li>export annotation rows as CSV for spreadsheet import</li>
410 <li>Jalview projects record alignment dataset associations, EMBL
411 products, and cDNA sequence mappings</li>
412 <li>Sequence Group colour can be specified in Annotation File</li>
413 <li>Ad-hoc colouring of group in Annotation File using RGB
414 triplet as name of colourscheme</li>
416 <em>VAMSAS Client capabilities (Experimental)</em>
418 <li>treenode binding for VAMSAS tree exchange</li>
419 <li>local editing and update of sequences in VAMSAS alignments
421 <li>Create new or select existing session to join</li>
422 <li>load and save of vamsas documents</li>
424 <em>Application command line</em>
426 <li>-tree parameter to open trees (introduced for passing from
428 <li>-fetchfrom command line argument to specify nicknames of DAS
429 servers to query for alignment features</li>
430 <li>-dasserver command line argument to add new servers that are
431 also automatically queried for features</li>
432 <li>-groovy command line argument executes a given groovy script
433 after all input data has been loaded and parsed</li>
435 <em>Applet-Application data exchange</em>
437 <li>Trees passed as applet parameters can be passed to
438 application (when using "View in full application")</li>
440 <em>Applet Parameters</em>
442 <li>feature group display control parameter</li>
443 <li>debug parameter</li>
444 <li>showbutton parameter</li>
446 <em>Applet API methods</em>
448 <li>newView public method</li>
449 <li>Window (current view) specific get/set public methods</li>
450 <li>Feature display control methods</li>
451 <li>get list of currently selected sequences</li>
453 <em>New Jalview distribution features</em>
455 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
456 <li>RELEASE file gives build properties for the latest Jalview
458 <li>Java 1.1 Applet build made easier and donotobfuscate
459 property controls execution of obfuscator</li>
460 <li>Build target for generating source distribution</li>
461 <li>Debug flag for javacc</li>
462 <li>.jalview_properties file is documented (slightly) in
463 jalview.bin.Cache</li>
464 <li>Continuous Build Integration for stable and development
465 version of Application, Applet and source distribution</li>
471 <li>selected region output includes visible annotations (for
472 certain formats)</li>
473 <li>edit label/displaychar contains existing label/char for
475 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
476 <li>shorter peptide product names from EMBL records</li>
477 <li>Newick string generator makes compact representations</li>
478 <li>bootstrap values parsed correctly for tree files with
480 <li>pathological filechooser bug avoided by not allowing
481 filenames containing a ':'</li>
482 <li>Fixed exception when parsing GFF files containing global
483 sequence features</li>
484 <li>Alignment datasets are finalized only when number of
485 references from alignment sequences goes to zero</li>
486 <li>Close of tree branch colour box without colour selection
487 causes cascading exceptions</li>
488 <li>occasional negative imgwidth exceptions</li>
489 <li>better reporting of non-fatal warnings to user when file
491 <li>Save works when Jalview project is default format</li>
492 <li>Save as dialog opened if current alignment format is not a
493 valid output format</li>
494 <li>Uniprot canonical names introduced for both das and vamsas</li>
495 <li>Histidine should be midblue (not pink!) in Zappo</li>
496 <li>error messages passed up and output when data read fails</li>
497 <li>edit undo recovers previous dataset sequence when sequence
499 <li>allow PDB files without pdb ID HEADER lines (like those
500 generated by MODELLER) to be read in properly</li>
501 <li>allow reading of JPred concise files as a normal filetype</li>
502 <li>Stockholm annotation parsing and alignment properties import
503 fixed for PFAM records</li>
504 <li>Structure view windows have correct name in Desktop window
506 <li>annotation consisting of sequence associated scores can be
507 read and written correctly to annotation file</li>
508 <li>Aligned cDNA translation to aligned peptide works correctly</li>
509 <li>Fixed display of hidden sequence markers and non-italic font
510 for representatives in Applet</li>
511 <li>Applet Menus are always embedded in applet window on Macs.</li>
512 <li>Newly shown features appear at top of stack (in Applet)</li>
513 <li>Annotations added via parameter not drawn properly due to
514 null pointer exceptions</li>
515 <li>Secondary structure lines are drawn starting from first
516 column of alignment</li>
517 <li>Uniprot XML import updated for new schema release in July
519 <li>Sequence feature to sequence ID match for Features file is
520 case-insensitive</li>
521 <li>Sequence features read from Features file appended to all
522 sequences with matching IDs</li>
523 <li>PDB structure coloured correctly for associated views
524 containing a sub-sequence</li>
525 <li>PDB files can be retrieved by applet from Jar files</li>
526 <li>feature and annotation file applet parameters referring to
527 different directories are retrieved correctly</li>
528 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
529 <li>Fixed application hang whilst waiting for splash-screen
530 version check to complete</li>
531 <li>Applet properly URLencodes input parameter values when
532 passing them to the launchApp service</li>
533 <li>display name and local features preserved in results
534 retrieved from web service</li>
535 <li>Visual delay indication for sequence retrieval and sequence
536 fetcher initialisation</li>
537 <li>updated Application to use DAS 1.53e version of dasobert DAS
539 <li>Re-instated Full AMSA support and .amsa file association</li>
540 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
547 <div align="center"><strong>2.3</strong><br>
552 <li>Jmol 11.0.2 integration</li>
553 <li>PDB views stored in Jalview XML files</li>
554 <li>Slide sequences</li>
555 <li>Edit sequence in place</li>
556 <li>EMBL CDS features</li>
557 <li>DAS Feature mapping</li>
558 <li>Feature ordering</li>
559 <li>Alignment Properties</li>
560 <li>Annotation Scores</li>
561 <li>Sort by scores</li>
562 <li>Feature/annotation editing in applet</li>
567 <li>Headless state operation in 2.2.1</li>
568 <li>Incorrect and unstable DNA pairwise alignment</li>
569 <li>Cut and paste of sequences with annotation</li>
570 <li>Feature group display state in XML</li>
571 <li>Feature ordering in XML</li>
572 <li>blc file iteration selection using filename # suffix</li>
573 <li>Stockholm alignment properties</li>
574 <li>Stockhom alignment secondary structure annotation</li>
575 <li>2.2.1 applet had no feature transparency</li>
576 <li>Number pad keys can be used in cursor mode</li>
577 <li>Structure Viewer mirror image resolved</li>
584 <div align="center"><strong>2.2.1</strong><br>
589 <li>Non standard characters can be read and displayed
590 <li>Annotations/Features can be imported/exported to the applet
592 <li>Applet allows editing of sequence/annotation/group name
594 <li>Preference setting to display sequence name in italics
595 <li>Annotation file format extended to allow Sequence_groups to
597 <li>Default opening of alignment overview panel can be specified
599 <li>PDB residue numbering annotation added to associated
605 <li>Applet crash under certain Linux OS with Java 1.6 installed
606 <li>Annotation file export / import bugs fixed
607 <li>PNG / EPS image output bugs fixed
613 <div align="center"><strong>2.2</strong><br>
618 <li>Multiple views on alignment
619 <li>Sequence feature editing
620 <li>"Reload" alignment
621 <li>"Save" to current filename
622 <li>Background dependent text colour
623 <li>Right align sequence ids
624 <li>User-defined lower case residue colours
627 <li>Menu item accelerator keys
628 <li>Control-V pastes to current alignment
629 <li>Cancel button for DAS Feature Fetching
630 <li>PCA and PDB Viewers zoom via mouse roller
631 <li>User-defined sub-tree colours and sub-tree selection
632 <li>'New Window' button on the 'Output to Text box'
637 <li>New memory efficient Undo/Redo System
638 <li>Optimised symbol lookups and conservation/consensus
640 <li>Region Conservation/Consensus recalculated after edits
641 <li>Fixed Remove Empty Columns Bug (empty columns at end of
643 <li>Slowed DAS Feature Fetching for increased robustness.
644 <li>Made angle brackets in ASCII feature descriptions display
646 <li>Re-instated Zoom function for PCA
647 <li>Sequence descriptions conserved in web service analysis
649 <li>Uniprot ID discoverer uses any word separated by ∣
650 <li>WsDbFetch query/result association resolved
651 <li>Tree leaf to sequence mapping improved
652 <li>Smooth fonts switch moved to FontChooser dialog box.
658 <div align="center"><strong>2.1.1</strong><br>
663 <li>Copy consensus sequence to clipboard</li>
668 <li>Image output - rightmost residues are rendered if sequence
669 id panel has been resized</li>
670 <li>Image output - all offscreen group boundaries are rendered</li>
671 <li>Annotation files with sequence references - all elements in
672 file are relative to sequence position</li>
673 <li>Mac Applet users can use Alt key for group editing</li>
679 <div align="center"><strong>2.1</strong><br>
684 <li>MAFFT Multiple Alignment in default Web Service list</li>
685 <li>DAS Feature fetching</li>
686 <li>Hide sequences and columns</li>
687 <li>Export Annotations and Features</li>
688 <li>GFF file reading / writing</li>
689 <li>Associate structures with sequences from local PDB files</li>
690 <li>Add sequences to exisiting alignment</li>
691 <li>Recently opened files / URL lists</li>
692 <li>Applet can launch the full application</li>
693 <li>Applet has transparency for features (Java 1.2 required)</li>
694 <li>Applet has user defined colours parameter</li>
695 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
700 <li>Redundancy Panel reinstalled in the Applet</li>
701 <li>Monospaced font - EPS / rescaling bug fixed</li>
702 <li>Annotation files with sequence references bug fixed</li>
708 <div align="center"><strong>2.08.1</strong><br>
713 <li>Change case of selected region from Popup menu</li>
714 <li>Choose to match case when searching</li>
715 <li>Middle mouse button and mouse movement can compress / expand
716 the visible width and height of the alignment</li>
721 <li>Annotation Panel displays complete JNet results</li>
727 <div align="center"><strong>2.08b</strong><br>
733 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
734 <li>Righthand label on wrapped alignments shows correct value</li>
740 <div align="center"><strong>2.08</strong><br>
745 <li>Editing can be locked to the selection area</li>
746 <li>Keyboard editing</li>
747 <li>Create sequence features from searches</li>
748 <li>Precalculated annotations can be loaded onto alignments</li>
749 <li>Features file allows grouping of features</li>
750 <li>Annotation Colouring scheme added</li>
751 <li>Smooth fonts off by default - Faster rendering</li>
752 <li>Choose to toggle Autocalculate Consensus On/Off</li>
757 <li>Drag & Drop fixed on Linux</li>
758 <li>Jalview Archive file faster to load/save, sequence
759 descriptions saved.</li>
765 <div align="center"><strong>2.07</strong><br>
770 <li>PDB Structure Viewer enhanced</li>
771 <li>Sequence Feature retrieval and display enhanced</li>
772 <li>Choose to output sequence start-end after sequence name for
774 <li>Sequence Fetcher WSDBFetch@EBI</li>
775 <li>Applet can read feature files, PDB files and can be used for
781 <li>HTML output writes groups and features</li>
782 <li>Group editing is Control and mouse click</li>
783 <li>File IO bugs</li>
789 <div align="center"><strong>2.06</strong><br>
794 <li>View annotations in wrapped mode</li>
795 <li>More options for PCA viewer</li>
800 <li>GUI bugs resolved</li>
801 <li>Runs with -nodisplay from command line</li>
807 <div align="center"><strong>2.05b</strong><br>
812 <li>Choose EPS export as lineart or text</li>
813 <li>Jar files are executable</li>
814 <li>Can read in Uracil - maps to unknown residue</li>
819 <li>Known OutOfMemory errors give warning message</li>
820 <li>Overview window calculated more efficiently</li>
821 <li>Several GUI bugs resolved</li>
827 <div align="center"><strong>2.05</strong><br>
832 <li>Edit and annotate in "Wrapped" view</li>
837 <li>Several GUI bugs resolved</li>
843 <div align="center"><strong>2.04</strong><br>
848 <li>Hold down mouse wheel & scroll to change font size</li>
853 <li>Improved JPred client reliability</li>
854 <li>Improved loading of Jalview files</li>
860 <div align="center"><strong>2.03</strong><br>
865 <li>Set Proxy server name and port in preferences</li>
866 <li>Multiple URL links from sequence ids</li>
867 <li>User Defined Colours can have a scheme name and added to
869 <li>Choose to ignore gaps in consensus calculation</li>
870 <li>Unix users can set default web browser</li>
871 <li>Runs without GUI for batch processing</li>
872 <li>Dynamically generated Web Service Menus</li>
877 <li>InstallAnywhere download for Sparc Solaris</li>
883 <div align="center"><strong>2.02</strong><br>
889 <li>Copy & Paste order of sequences maintains alignment
896 <div align="center"><strong>2.01</strong><br>
901 <li>Use delete key for deleting selection.</li>
902 <li>Use Mouse wheel to scroll sequences.</li>
903 <li>Help file updated to describe how to add alignment
905 <li>Version and build date written to build properties file.</li>
906 <li>InstallAnywhere installation will check for updates at
907 launch of Jalview.</li>
912 <li>Delete gaps bug fixed.</li>
913 <li>FileChooser sorts columns.</li>
914 <li>Can remove groups one by one.</li>
915 <li>Filechooser icons installed.</li>
916 <li>Finder ignores return character when searching. Return key
917 will initiate a search.<br>
924 <div align="center"><strong>2.0</strong><br>
929 <li>New codebase</li>