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>
39 <strong><a name="Jalview2.7">2.7</a>
40 </strong><br> <em>20/09/2011</em>
42 <td><em>Application</em>
44 <li>tweaked default layout of web services menu</li>
45 <li>view/alignment association menu to enable user to easily
46 specify which alignment a multi-structure view takes its
47 colours/correspondences from</li>
48 <li>allow properties file location to be specified as URL </li>
49 <li>extend jalview project to preserve associations between
50 many alignment views and a single Jmol display</li>
51 <li>Store annotation row height in jalview project file</li>
52 <li>annotation row column label formatting attributes stored
54 <li>annotation row order for auto-calculated annotation rows
55 preserved in jalview project file</li>
56 <li>visual progress indication when Jalview state is saved
57 using Desktop window menu</li>
58 <li>visual indication that command line arguments are still
60 <li>groovy script execution from URL</li>
61 <li>colour by annotation default min and max colours in
63 <li>automatically associate PDB files dragged onto an
64 alignment with sequences that have high similarity and matching
66 <li>update JGoogleAnalytics to latest release (0.3)</li>
67 <li>'view structures' option to open many structures
69 <li>Sort associated views menu option for tree panel</li>
70 <li>group all JABA and non-JABA services for a particular
71 analysis function in its own submenu</li>
74 <li>userdefined and autogenerated annotation rows for groups</li>
75 <li>adjustment of alignment annotation pane height</li>
76 <li>annotation scrollbar for annotation panel</li>
77 <li>drag to reorder annotation rows in annotation panel</li>
78 <li>'automaticScrolling' parameter</li>
79 <li>allow sequences with partial ID string matches to be
80 annotated from GFF/jalview features files</li>
81 <li>sequence logo annotation row in applet</li>
82 <li>Absolute paths relative to host server in applet
83 parameters are treated as such</li>
84 <li>New in the JalviewLite javascript API:
86 <li>jalviewLite.js javascript library</li>
87 <li>Javascript callbacks for
89 <li>applet initialisation</li>
90 <li>sequence/alignment mouse-overs and selections</li>
93 <li>scrollTo row and column alignment scrolling functions</li>
94 <li>select sequence/alignment regions from javascript</li>
95 <li>javascript structure viewer harness to pass messages
96 between Jmol and Jalview when running as distinct applets</li>
97 <li>sortBy method</li>
98 <li>set of applet and application examples shipped with
100 <li>new example to demonstrate jalviewLite and Jmol
101 javascript message exchange</li>
103 </ul> <em>General</em>
105 <li>enable Jmol displays to be associated with multiple
106 multiple alignments</li>
107 <li>Option to automatically sort alignment with new tree</li>
108 <li>user configurable link to enable redirects to a
109 www.jalview.org mirror</li>
110 <li>Jmol colours option for Jmol displays</li>
111 <li>configurable newline string when writing alignment and
112 other flat files</li>
113 <li>Allow alignment annotation description lines to contain
115 </ul> <em>Documentation and Development</em>
117 <li>add groovy test harness for bulk load testing to examples
119 <li>groovy script to load and align a set of sequences using a
120 web service before displaying the result in the Jalview desktop</li>
121 <li>restructured javascript and applet api documentation</li>
122 <li>ant target to publish example html files with applet archive</li>
123 <li>netbeans project for building jalview from source</li>
124 <li>ant task to create online javadoc for jalview source</li>
126 <td><em>Application</em>
128 <li>user defined colourscheme throws exception when current
129 built in colourscheme is saved as new scheme</li>
130 <li>AlignFrame->Save in application pops up save dialog for
131 valid filename/format</li>
132 <li>cannot view associated structure for uniprot sequence</li>
133 <li>pdb file association breaks for Uniprot sequence P37173</li>
134 <li>associate PDB from file dialog does not tell you which
135 sequence is to be associated with the file</li>
136 <li>find All raises null pointer exception when query only
137 matches sequence IDs</li>
138 <li>pre 2.6 jalview project cannot be loaded into v2.6</li>
139 <li>Jalview project with Jmol views created with Jalview 2.4
140 cannot be loaded</li>
141 <li>filetype associations not installed for webstart launch</li>
142 <li>two or more chains in a single PDB file associated with
143 sequences in different alignments do not get coloured by their
144 associated sequence</li>
145 <li>visibility status of autocalculated annotation row not
146 preserved when project is loaded</li>
147 <li>tree bootstraps are not preserved when saved as a jalview
149 <li>envision2 workflow tooltips are corrupted</li>
150 <li>enabling show group conservation also enables colour by
152 <li>duplicate group associated conservation or consensus
153 created on new view</li>
154 <li>annotation scrollbar not displayed after 'show all
155 hidden annotation rows' option selected</li>
156 <li>alignment quality not updated after alignment annotation
157 row is hidden then shown</li>
158 <li>preserve colouring of structures coloured by sequences in pre
159 jalview 2.7 projects</li>
160 <li>Web service job parameter dialog is not laid out properly
162 <li>web services menu not refreshed after 'reset
163 services' button is pressed in preferences</li>
164 <li>annotation off by one in jalview v2_3 example project</li>
165 <li>structures imported from file and saved in project get
166 name like jalview_pdb1234.txt when reloaded</li>
167 <li>Jalview does not always retrieve progress of a JABAWS job
168 execution in full once it is complete</li>
169 </ul> <em>Applet</em>
171 <li>alignment height set incorrectly when lots of annotation
172 rows are displayed</li>
173 <li>relative URLs in feature HTML text not resolved to
175 <li>view follows highlighting does not work for positions in
177 <li><= shown as = in tooltip</li>
178 <li>export features raises exception when no features exist</li>
179 <li>separator string used for serialising lists of ids for
180 javascript api is modified when separator string provided as
182 <li>null pointer exception when selecting tree leaves for
183 alignment with no existing selection</li>
184 <li>relative URLs for datasources assumed to be relative to
185 applet's codebase</li>
186 <li>status bar not updated after finished searching and search
187 wraps around to first result</li>
188 <li>StructureSelectionManager instance shared between several
189 jalview applets causes race conditions and memory leaks</li>
190 <li>hover tooltip and mouseover of position on structure not
191 sent from Jmol in applet</li>
192 <li>certain sequences of javascript method calls to applet API
193 fatally hang browser</li>
194 </ul> <em>General</em>
196 <li>view follows structure mouseover scrolls beyond position
197 with wrapped view and hidden regions</li>
198 <li>Find sequence position moves to wrong residue with/without
200 <li>Sequence length given in alignment properties window is
202 <li>InvalidNumberFormat exceptions thrown when trying to
203 import PDB like structure files</li>
204 <li>positional search results are only highlighted between
205 user-supplied sequence start/end bounds</li>
206 <li>end attribute of sequence is not validated</li>
207 <li>Find dialog only finds first sequence containing a given
208 sequence position</li>
209 <li>sequence numbering not preserved in MSF alignment output</li>
210 <li>Jalview PDB file reader does not extract sequence from
211 nucleotide chains correctly</li>
212 <li>annotation row height and visibility attributes not stored
213 in jalview project</li>
214 <li>structure colours not updated when tree partition changed
216 <li>sequence associated secondary structure not correctly
217 parsed in interleaved stockholm</li>
218 <li>colour by annotation dialog does not restore current state
220 <li>Hiding (nearly) all sequences doesn't work properly</li>
221 <li>sequences containing lowercase letters are not properly
222 associated with their pdb files</li>
223 </ul> <em>Documentation and Development</em>
225 <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
232 <strong><a name="Jalview2.6.1">2.6.1</a>
233 </strong><br> <em>15/11/2010</em>
235 <td><em>Application</em>
237 <li>New warning dialog when the Jalview Desktop cannot contact
239 <li>JABA service parameters for a preset are shown in service
241 <li>JABA Service menu entries reworded</li>
245 <li>Modeller PIR IO broken - cannot correctly import a pir
246 file emitted by jalview</li>
247 <li>Existing feature settings transferred to new alignment
248 view created from cut'n'paste</li>
249 <li>Improved test for mixed amino/nucleotide chains when
250 parsing PDB files</li>
251 <li>Consensus and conservation annotation rows occasionally
252 become blank for all new windows</li>
253 <li>Exception raised when right clicking above sequences in
254 wrapped view mode</li>
255 </ul> <em>Application</em>
257 <li>multiple multiply aligned structure views cause cpu usage
258 to hit 100% and computer to hang</li>
259 <li>Web Service parameter layout breaks for long user
261 <li>Jaba service discovery hangs desktop if Jaba server is
267 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
268 <em>26/9/2010</em></div>
270 <td><em>Application</em>
272 <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
273 <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
274 <li>Web Services preference tab</li>
275 <li>Analysis parameters dialog box and user defined preferences</li>
276 <li>Improved speed and layout of Envision2 service menu</li>
277 <li>Superpose structures using associated sequence alignment</li>
278 <li>Export coordinates and projection as CSV from PCA viewer</li>
282 <li>enable javascript: execution by the applet via the link out
287 <li>Updated the Jmol Jalview interface to work with Jmol series
289 <li>The Jalview Desktop and JalviewLite applet now require Java
291 <li>Allow Jalview feature colour specification for GFF sequence
292 annotation files</li>
293 <li>New 'colour by label' keword in jalview feature file type
294 colour specification</li>
295 <li>New Jalview Desktop Groovy API method that allows a script
296 to check if it being run in an interactive session or in a batch
297 operation from the jalview command line</li>
302 <li>clustalx colourscheme colours Ds preferentially when both
303 D+E are present in over 50% of the column</li>
308 <li>typo in AlignmentFrame->View->Hide->all but
309 selected Regions menu item</li>
310 <li>sequence fetcher replaces ',' for ';' when the ',' is part
311 of a valid accession ID</li>
312 <li>fatal OOM if object retrieved by sequence fetcher runs out
314 <li>unhandled Out of Memory Error when viewing pca analysis
316 <li>InstallAnywhere builds fail to launch on OS X java 10.5
317 update 4 (due to apple Java 1.6 update)</li>
318 <li>Installanywhere Jalview silently fails to launch</li>
322 <li>Jalview.getFeatureGroups() raises an
323 ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
329 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
330 <em>14/6/2010</em></div>
335 <li>Alignment prettyprinter doesn't cope with long sequence IDs
337 <li>clustalx colourscheme colours Ds preferentially when both
338 D+E are present in over 50% of the column</li>
339 <li>nucleic acid structures retrieved from PDB do not import
341 <li>More columns get selected than were clicked on when a number
342 of columns are hidden</li>
343 <li>annotation label popup menu not providing correct
344 add/hide/show options when rows are hidden or none are present</li>
345 <li>Stockholm format shown in list of readable formats, and
346 parser copes better with alignments from RFAM.</li>
347 <li>CSV output of consensus only includes the percentage of all
348 symbols if sequence logo display is enabled</li>
353 <li>annotation panel disappears when annotation is
358 <li>Alignment view not redrawn properly when new alignment
359 opened where annotation panel is visible but no annotations are
360 present on alignment</li>
361 <li>pasted region containing hidden columns is incorrectly
362 displayed in new alignment window</li>
363 <li>Jalview slow to complete operations when stdout is flooded
364 (fix is to close the Jalview console)</li>
365 <li>typo in AlignmentFrame->View->Hide->all but
366 selected Rregions menu item.</li>
367 <li>inconsistent group submenu and Format submenu entry 'Un' or
369 <li>Sequence feature settings are being shared by multiple
370 distinct alignments</li>
371 <li>group annotation not recreated when tree partition is
373 <li>double click on group annotation to select sequences does
374 not propagate to associated trees</li>
375 <li>Mac OSX specific issues:
377 <li>exception raised when mouse clicked on desktop window
379 <li>Desktop menu placed on menu bar and application name set
381 <li>sequence feature settings not wide enough for the save
382 feature colourscheme button</li>
391 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
392 <em>30/4/2010</em></div>
394 <td><em>New Capabilities</em>
396 <li>URL links generated from description line for
397 regular-expression based URL links (applet and application)
398 <li>Non-positional feature URL links are shown in link menu</li>
399 <li>Linked viewing of nucleic acid sequences and structures</li>
400 <li>Automatic Scrolling option in View menu to display the
401 currently highlighted region of an alignment.</li>
402 <li>Order an alignment by sequence length, or using the average
403 score or total feature count for each sequence.</li>
404 <li>Shading features by score or associated description</li>
405 <li>Subdivide alignment and groups based on identity of selected
406 subsequence (Make Groups from Selection).</li>
407 <li>New hide/show options including Shift+Control+H to hide
408 everything but the currently selected region.</li>
409 <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
413 <li>Fetch DB References capabilities and UI expanded to support
414 retrieval from DAS sequence sources</li>
415 <li>Local DAS Sequence sources can be added via the command line
416 or via the Add local source dialog box.</li>
417 <li>DAS Dbref and DbxRef feature types are parsed as database
418 references and protein_name is parsed as description line (BioSapiens
420 <li>Enable or disable non-positional feature and database
421 references in sequence ID tooltip from View menu in application.</li>
422 <!-- <li>New hidden columns and rows and representatives capabilities
423 in annotations file (in progress - not yet fully implemented)</li> -->
424 <li>Group-associated consensus, sequence logos and conservation
426 <li>Symbol distributions for each column can be exported and
427 visualized as sequence logos</li>
428 <li>Optionally scale multi-character column labels to fit within
429 each column of annotation row<!-- todo for applet --></li>
430 <li>Optional automatic sort of associated alignment view when a
431 new tree is opened.</li>
432 <li>Jalview Java Console</li>
433 <li>Better placement of desktop window when moving between
434 different screens.</li>
435 <li>New preference items for sequence ID tooltip and consensus
437 <li>Client to submit sequences and IDs to <a
438 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
439 <li><em>Vamsas Capabilities</em>
441 <li>Improved VAMSAS synchronization (jalview archive used to
442 preserve views, structures, and tree display settings)</li>
443 <li>Import of vamsas documents from disk or URL via command
445 <li>Sharing of selected regions between views and with other
446 VAMSAS applications (Experimental feature!)</li>
447 <li>Updated API to VAMSAS version 0.2</li>
453 <li>Middle button resizes annotation row height</li>
456 <li>sortByTree (true/false) - automatically sort the associated
457 alignment view by the tree when a new tree is opened.</li>
458 <li>showTreeBootstraps (true/false) - show or hide branch
459 bootstraps (default is to show them if available)</li>
460 <li>showTreeDistances (true/false) - show or hide branch
461 lengths (default is to show them if available)</li>
462 <li>showUnlinkedTreeNodes (true/false) - indicate if
463 unassociated nodes should be highlighted in the tree view</li>
464 <li>heightScale and widthScale (1.0 or more) - increase the
465 height or width of a cell in the alignment grid relative to the
466 current font size.</li>
469 <li>Non-positional features displayed in sequence ID tooltip</li>
473 <li>Features format: graduated colour definitions and
474 specification of feature scores</li>
475 <li>Alignment Annotations format: new keywords for group
476 associated annotation (GROUP_REF) and annotation row display
477 properties (ROW_PROPERTIES)</li>
478 <li>XML formats extended to support graduated feature
479 colourschemes, group associated annotation, and profile visualization
484 <li>Source field in GFF files parsed as feature source rather
485 than description</li>
486 <li>Non-positional features are now included in sequence feature
487 and gff files (controlled via non-positional feature visibility in
489 <li>URL links generated for all feature links (bugfix)</li>
490 <li>Added URL embedding instructions to features file
492 <li>Codons containing ambiguous nucleotides translated as 'X' in
494 <li>Match case switch in find dialog box works for both sequence
495 ID and sequence string and query strings do not have to be in upper
496 case to match case-insensitively.</li>
497 <li>AMSA files only contain first column of multi-character
498 column annotation labels</li>
499 <li>Jalview Annotation File generation/parsing consistent with
500 documentation (e.g. Stockholm annotation can be exported and
502 <li>PDB files without embedded PDB IDs given a friendly name</li>
503 <li>Find incrementally searches ID string matches as well as
504 subsequence matches, and correctly reports total number of both.</li>
507 <li>Better handling of exceptions during sequence retrieval</li>
508 <li>Dasobert generated non-positional feature URL link text
509 excludes the start_end suffix</li>
510 <li>DAS feature and source retrieval buttons disabled when
511 fetch or registry operations in progress.</li>
512 <li>PDB files retrieved from URLs are cached properly</li>
513 <li>Sequence description lines properly shared via VAMSAS</li>
514 <li>Sequence fetcher fetches multiple records for all data
516 <li>Ensured that command line das feature retrieval completes
517 before alignment figures are generated.</li>
518 <li>Reduced time taken when opening file browser for first
520 <li>isAligned check prior to calculating tree, PCA or
521 submitting an MSA to JNet now excludes hidden sequences.</li>
522 <li>User defined group colours properly recovered from Jalview
532 <div align="center"><strong>2.4.0.b2</strong><br>
537 <li>Experimental support for google analytics usage tracking.</li>
538 <li>Jalview privacy settings (user preferences and docs).</li>
543 <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
544 <li>Exception when feature created from selection beyond length
546 <li>Allow synthetic PDB files to be imported gracefully</li>
547 <li>Sequence associated annotation rows associate with all
548 sequences with a given id</li>
549 <li>Find function matches case-insensitively for sequence ID
551 <li>Non-standard characters do not cause pairwise alignment to
552 fail with exception</li>
554 <em>Application Issues</em>
556 <li>Sequences are now validated against EMBL database</li>
557 <li>Sequence fetcher fetches multiple records for all data
560 <em>InstallAnywhere Issues</em>
562 <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
563 installAnywhere mechanism)</li>
564 <li>Command line launching of JARs from InstallAnywhere version
565 (java class versioning error fixed)</li>
572 <div align="center"><strong>2.4</strong><br>
575 <td><em>User Interface</em>
577 <li>Linked highlighting of codon and amino acid from translation
578 and protein products</li>
579 <li>Linked highlighting of structure associated with residue
580 mapping to codon position</li>
581 <li>Sequence Fetcher provides example accession numbers and
583 <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
584 <li>Extract score function to parse whitespace separated numeric
585 data in description line</li>
586 <li>Column labels in alignment annotation can be centred.</li>
587 <li>Tooltip for sequence associated annotation give name of
590 <em>Web Services and URL fetching</em>
592 <li>JPred3 web service</li>
593 <li>Prototype sequence search client (no public services
595 <li>Fetch either seed alignment or full alignment from PFAM</li>
596 <li>URL Links created for matching database cross references as
597 well as sequence ID</li>
598 <li>URL Links can be created using regular-expressions</li>
600 <em>Sequence Database Connectivity</em>
602 <li>Retrieval of cross-referenced sequences from other databases
604 <li>Generalised database reference retrieval and validation to
605 all fetchable databases</li>
606 <li>Fetch sequences from DAS sources supporting the sequence
609 <em>Import and Export</em>
610 <li>export annotation rows as CSV for spreadsheet import</li>
611 <li>Jalview projects record alignment dataset associations, EMBL
612 products, and cDNA sequence mappings</li>
613 <li>Sequence Group colour can be specified in Annotation File</li>
614 <li>Ad-hoc colouring of group in Annotation File using RGB
615 triplet as name of colourscheme</li>
617 <em>VAMSAS Client capabilities (Experimental)</em>
619 <li>treenode binding for VAMSAS tree exchange</li>
620 <li>local editing and update of sequences in VAMSAS alignments
622 <li>Create new or select existing session to join</li>
623 <li>load and save of vamsas documents</li>
625 <em>Application command line</em>
627 <li>-tree parameter to open trees (introduced for passing from
629 <li>-fetchfrom command line argument to specify nicknames of DAS
630 servers to query for alignment features</li>
631 <li>-dasserver command line argument to add new servers that are
632 also automatically queried for features</li>
633 <li>-groovy command line argument executes a given groovy script
634 after all input data has been loaded and parsed</li>
636 <em>Applet-Application data exchange</em>
638 <li>Trees passed as applet parameters can be passed to
639 application (when using "View in full application")</li>
641 <em>Applet Parameters</em>
643 <li>feature group display control parameter</li>
644 <li>debug parameter</li>
645 <li>showbutton parameter</li>
647 <em>Applet API methods</em>
649 <li>newView public method</li>
650 <li>Window (current view) specific get/set public methods</li>
651 <li>Feature display control methods</li>
652 <li>get list of currently selected sequences</li>
654 <em>New Jalview distribution features</em>
656 <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
657 <li>RELEASE file gives build properties for the latest Jalview
659 <li>Java 1.1 Applet build made easier and donotobfuscate
660 property controls execution of obfuscator</li>
661 <li>Build target for generating source distribution</li>
662 <li>Debug flag for javacc</li>
663 <li>.jalview_properties file is documented (slightly) in
664 jalview.bin.Cache</li>
665 <li>Continuous Build Integration for stable and development
666 version of Application, Applet and source distribution</li>
672 <li>selected region output includes visible annotations (for
673 certain formats)</li>
674 <li>edit label/displaychar contains existing label/char for
676 <li>update PDBEntries when DBRefEntries change (vamsas)</li>
677 <li>shorter peptide product names from EMBL records</li>
678 <li>Newick string generator makes compact representations</li>
679 <li>bootstrap values parsed correctly for tree files with
681 <li>pathological filechooser bug avoided by not allowing
682 filenames containing a ':'</li>
683 <li>Fixed exception when parsing GFF files containing global
684 sequence features</li>
685 <li>Alignment datasets are finalized only when number of
686 references from alignment sequences goes to zero</li>
687 <li>Close of tree branch colour box without colour selection
688 causes cascading exceptions</li>
689 <li>occasional negative imgwidth exceptions</li>
690 <li>better reporting of non-fatal warnings to user when file
692 <li>Save works when Jalview project is default format</li>
693 <li>Save as dialog opened if current alignment format is not a
694 valid output format</li>
695 <li>Uniprot canonical names introduced for both das and vamsas</li>
696 <li>Histidine should be midblue (not pink!) in Zappo</li>
697 <li>error messages passed up and output when data read fails</li>
698 <li>edit undo recovers previous dataset sequence when sequence
700 <li>allow PDB files without pdb ID HEADER lines (like those
701 generated by MODELLER) to be read in properly</li>
702 <li>allow reading of JPred concise files as a normal filetype</li>
703 <li>Stockholm annotation parsing and alignment properties import
704 fixed for PFAM records</li>
705 <li>Structure view windows have correct name in Desktop window
707 <li>annotation consisting of sequence associated scores can be
708 read and written correctly to annotation file</li>
709 <li>Aligned cDNA translation to aligned peptide works correctly</li>
710 <li>Fixed display of hidden sequence markers and non-italic font
711 for representatives in Applet</li>
712 <li>Applet Menus are always embedded in applet window on Macs.</li>
713 <li>Newly shown features appear at top of stack (in Applet)</li>
714 <li>Annotations added via parameter not drawn properly due to
715 null pointer exceptions</li>
716 <li>Secondary structure lines are drawn starting from first
717 column of alignment</li>
718 <li>Uniprot XML import updated for new schema release in July
720 <li>Sequence feature to sequence ID match for Features file is
721 case-insensitive</li>
722 <li>Sequence features read from Features file appended to all
723 sequences with matching IDs</li>
724 <li>PDB structure coloured correctly for associated views
725 containing a sub-sequence</li>
726 <li>PDB files can be retrieved by applet from Jar files</li>
727 <li>feature and annotation file applet parameters referring to
728 different directories are retrieved correctly</li>
729 <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
730 <li>Fixed application hang whilst waiting for splash-screen
731 version check to complete</li>
732 <li>Applet properly URLencodes input parameter values when
733 passing them to the launchApp service</li>
734 <li>display name and local features preserved in results
735 retrieved from web service</li>
736 <li>Visual delay indication for sequence retrieval and sequence
737 fetcher initialisation</li>
738 <li>updated Application to use DAS 1.53e version of dasobert DAS
740 <li>Re-instated Full AMSA support and .amsa file association</li>
741 <li>Fixed parsing of JNet Concise annotation <em>sans</em>
748 <div align="center"><strong>2.3</strong><br>
753 <li>Jmol 11.0.2 integration</li>
754 <li>PDB views stored in Jalview XML files</li>
755 <li>Slide sequences</li>
756 <li>Edit sequence in place</li>
757 <li>EMBL CDS features</li>
758 <li>DAS Feature mapping</li>
759 <li>Feature ordering</li>
760 <li>Alignment Properties</li>
761 <li>Annotation Scores</li>
762 <li>Sort by scores</li>
763 <li>Feature/annotation editing in applet</li>
768 <li>Headless state operation in 2.2.1</li>
769 <li>Incorrect and unstable DNA pairwise alignment</li>
770 <li>Cut and paste of sequences with annotation</li>
771 <li>Feature group display state in XML</li>
772 <li>Feature ordering in XML</li>
773 <li>blc file iteration selection using filename # suffix</li>
774 <li>Stockholm alignment properties</li>
775 <li>Stockhom alignment secondary structure annotation</li>
776 <li>2.2.1 applet had no feature transparency</li>
777 <li>Number pad keys can be used in cursor mode</li>
778 <li>Structure Viewer mirror image resolved</li>
785 <div align="center"><strong>2.2.1</strong><br>
790 <li>Non standard characters can be read and displayed
791 <li>Annotations/Features can be imported/exported to the applet
793 <li>Applet allows editing of sequence/annotation/group name
795 <li>Preference setting to display sequence name in italics
796 <li>Annotation file format extended to allow Sequence_groups to
798 <li>Default opening of alignment overview panel can be specified
800 <li>PDB residue numbering annotation added to associated
806 <li>Applet crash under certain Linux OS with Java 1.6 installed
807 <li>Annotation file export / import bugs fixed
808 <li>PNG / EPS image output bugs fixed
814 <div align="center"><strong>2.2</strong><br>
819 <li>Multiple views on alignment
820 <li>Sequence feature editing
821 <li>"Reload" alignment
822 <li>"Save" to current filename
823 <li>Background dependent text colour
824 <li>Right align sequence ids
825 <li>User-defined lower case residue colours
828 <li>Menu item accelerator keys
829 <li>Control-V pastes to current alignment
830 <li>Cancel button for DAS Feature Fetching
831 <li>PCA and PDB Viewers zoom via mouse roller
832 <li>User-defined sub-tree colours and sub-tree selection
833 <li>'New Window' button on the 'Output to Text box'
838 <li>New memory efficient Undo/Redo System
839 <li>Optimised symbol lookups and conservation/consensus
841 <li>Region Conservation/Consensus recalculated after edits
842 <li>Fixed Remove Empty Columns Bug (empty columns at end of
844 <li>Slowed DAS Feature Fetching for increased robustness.
845 <li>Made angle brackets in ASCII feature descriptions display
847 <li>Re-instated Zoom function for PCA
848 <li>Sequence descriptions conserved in web service analysis
850 <li>Uniprot ID discoverer uses any word separated by ∣
851 <li>WsDbFetch query/result association resolved
852 <li>Tree leaf to sequence mapping improved
853 <li>Smooth fonts switch moved to FontChooser dialog box.
859 <div align="center"><strong>2.1.1</strong><br>
864 <li>Copy consensus sequence to clipboard</li>
869 <li>Image output - rightmost residues are rendered if sequence
870 id panel has been resized</li>
871 <li>Image output - all offscreen group boundaries are rendered</li>
872 <li>Annotation files with sequence references - all elements in
873 file are relative to sequence position</li>
874 <li>Mac Applet users can use Alt key for group editing</li>
880 <div align="center"><strong>2.1</strong><br>
885 <li>MAFFT Multiple Alignment in default Web Service list</li>
886 <li>DAS Feature fetching</li>
887 <li>Hide sequences and columns</li>
888 <li>Export Annotations and Features</li>
889 <li>GFF file reading / writing</li>
890 <li>Associate structures with sequences from local PDB files</li>
891 <li>Add sequences to exisiting alignment</li>
892 <li>Recently opened files / URL lists</li>
893 <li>Applet can launch the full application</li>
894 <li>Applet has transparency for features (Java 1.2 required)</li>
895 <li>Applet has user defined colours parameter</li>
896 <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
901 <li>Redundancy Panel reinstalled in the Applet</li>
902 <li>Monospaced font - EPS / rescaling bug fixed</li>
903 <li>Annotation files with sequence references bug fixed</li>
909 <div align="center"><strong>2.08.1</strong><br>
914 <li>Change case of selected region from Popup menu</li>
915 <li>Choose to match case when searching</li>
916 <li>Middle mouse button and mouse movement can compress / expand
917 the visible width and height of the alignment</li>
922 <li>Annotation Panel displays complete JNet results</li>
928 <div align="center"><strong>2.08b</strong><br>
934 <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
935 <li>Righthand label on wrapped alignments shows correct value</li>
941 <div align="center"><strong>2.08</strong><br>
946 <li>Editing can be locked to the selection area</li>
947 <li>Keyboard editing</li>
948 <li>Create sequence features from searches</li>
949 <li>Precalculated annotations can be loaded onto alignments</li>
950 <li>Features file allows grouping of features</li>
951 <li>Annotation Colouring scheme added</li>
952 <li>Smooth fonts off by default - Faster rendering</li>
953 <li>Choose to toggle Autocalculate Consensus On/Off</li>
958 <li>Drag & Drop fixed on Linux</li>
959 <li>Jalview Archive file faster to load/save, sequence
960 descriptions saved.</li>
966 <div align="center"><strong>2.07</strong><br>
971 <li>PDB Structure Viewer enhanced</li>
972 <li>Sequence Feature retrieval and display enhanced</li>
973 <li>Choose to output sequence start-end after sequence name for
975 <li>Sequence Fetcher WSDBFetch@EBI</li>
976 <li>Applet can read feature files, PDB files and can be used for
982 <li>HTML output writes groups and features</li>
983 <li>Group editing is Control and mouse click</li>
984 <li>File IO bugs</li>
990 <div align="center"><strong>2.06</strong><br>
995 <li>View annotations in wrapped mode</li>
996 <li>More options for PCA viewer</li>
1001 <li>GUI bugs resolved</li>
1002 <li>Runs with -nodisplay from command line</li>
1008 <div align="center"><strong>2.05b</strong><br>
1013 <li>Choose EPS export as lineart or text</li>
1014 <li>Jar files are executable</li>
1015 <li>Can read in Uracil - maps to unknown residue</li>
1020 <li>Known OutOfMemory errors give warning message</li>
1021 <li>Overview window calculated more efficiently</li>
1022 <li>Several GUI bugs resolved</li>
1028 <div align="center"><strong>2.05</strong><br>
1033 <li>Edit and annotate in "Wrapped" view</li>
1038 <li>Several GUI bugs resolved</li>
1044 <div align="center"><strong>2.04</strong><br>
1049 <li>Hold down mouse wheel & scroll to change font size</li>
1054 <li>Improved JPred client reliability</li>
1055 <li>Improved loading of Jalview files</li>
1061 <div align="center"><strong>2.03</strong><br>
1066 <li>Set Proxy server name and port in preferences</li>
1067 <li>Multiple URL links from sequence ids</li>
1068 <li>User Defined Colours can have a scheme name and added to
1070 <li>Choose to ignore gaps in consensus calculation</li>
1071 <li>Unix users can set default web browser</li>
1072 <li>Runs without GUI for batch processing</li>
1073 <li>Dynamically generated Web Service Menus</li>
1078 <li>InstallAnywhere download for Sparc Solaris</li>
1084 <div align="center"><strong>2.02</strong><br>
1090 <li>Copy & Paste order of sequences maintains alignment
1097 <div align="center"><strong>2.01</strong><br>
1102 <li>Use delete key for deleting selection.</li>
1103 <li>Use Mouse wheel to scroll sequences.</li>
1104 <li>Help file updated to describe how to add alignment
1106 <li>Version and build date written to build properties file.</li>
1107 <li>InstallAnywhere installation will check for updates at
1108 launch of Jalview.</li>
1113 <li>Delete gaps bug fixed.</li>
1114 <li>FileChooser sorts columns.</li>
1115 <li>Can remove groups one by one.</li>
1116 <li>Filechooser icons installed.</li>
1117 <li>Finder ignores return character when searching. Return key
1118 will initiate a search.<br>
1125 <div align="center"><strong>2.0</strong><br>
1130 <li>New codebase</li>