92cc453223be92895a18ae464df40223b7620b56
[jalview.git] / help / html / releases.html
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2 <!--
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
5  * 
6  * This file is part of Jalview.
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15  * PURPOSE.  See the GNU General Public License for more details.
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18 -->
19 <head>
20 <title>Release History</title>
21 </head>
22 <body>
23 <p><strong>Release History</strong></p>
24 <table border="1">
25         <tr>
26                 <td width="60" nowrap>
27                 <div align="center"><em><strong>Release</strong></em></div>
28                 </td>
29                 <td>
30                 <div align="center"><em><strong>New Features</strong></em></div>
31                 </td>
32                 <td>
33                 <div align="center"><em><strong>Issues Resolved</strong></em></div>
34                 </td>
35         </tr>
36         <tr>
37             <td>
38                 <div align="center"><strong><a name="Jalview2.6.1">2.6.1</a></strong><br>
39                 <em>15/11/2010</em></div>
40                 </td>
41                 <td><em>Application</em>
42                 <ul>
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>
46 </ul>
47                 </td>
48                 <td>
49                 <ul>
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>
55                 </ul>
56                 <em>Application</em>
57                 <ul>
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>
61     </ul>
62         </td>
63         </tr>
64         <tr>
65                 <td>
66                 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
67                 <em>26/9/2010</em></div>
68                 </td>
69                 <td><em>Application</em>
70                 <ul>
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>
78                 </ul>
79                 <em>Applet</em>
80                 <ul>
81                         <li>enable javascript: execution by the applet via the link out
82                         mechanism</li>
83                 </ul>
84                 <em>Other</em>
85                 <ul>
86                         <li>Updated the Jmol Jalview interface to work with Jmol series
87                         12</li>
88                         <li>The Jalview Desktop and JalviewLite applet now require Java
89                         1.5</li>
90                         <li>Allow Jalview feature colour specification for GFF sequence
91                         annotation files</li>
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>
97                 </ul>
98                 </td>
99                 <td>
100                 <ul>
101                         <li>clustalx colourscheme colours Ds preferentially when both
102                         D+E are present in over 50% of the column</li>
103                 </ul>
104
105                 <em>Application</em>
106                 <ul>
107                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;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
112                         of memory</li>
113                         <li>unhandled Out of Memory Error when viewing pca analysis
114                         results</li>
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>
118                 </ul>
119                 <em>Applet</em>
120                 <ul>
121                         <li>Jalview.getFeatureGroups() raises an
122                         ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
123                 </ul>
124                 </td>
125         </tr>
126         <tr>
127                 <td>
128                 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
129                 <em>14/6/2010</em></div>
130                 </td>
131                 <td></td>
132                 <td>
133                 <ul>
134                         <li>Alignment prettyprinter doesn't cope with long sequence IDs
135                         </li>
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
139                         correctly</li>
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>
148
149                 </ul>
150                 <em>Applet</em>
151                 <ul>
152                         <li>annotation panel disappears when annotation is
153                         hidden/removed</li>
154                 </ul>
155                 <em>Application</em>
156                 <ul>
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-&gt;View-&gt;Hide-&gt;all but
165                         selected Rregions menu item.</li>
166                         <li>inconsistent group submenu and Format submenu entry 'Un' or
167                         'Non'conserved</li>
168                         <li>Sequence feature settings are being shared by multiple
169                         distinct alignments</li>
170                         <li>group annotation not recreated when tree partition is
171                         changed</li>
172                         <li>double click on group annotation to select sequences does
173                         not propagate to associated trees</li>
174                         <li>Mac OSX specific issues:
175                         <ul>
176                                 <li>exception raised when mouse clicked on desktop window
177                                 background</li>
178                                 <li>Desktop menu placed on menu bar and application name set
179                                 correctly</li>
180                                 <li>sequence feature settings not wide enough for the save
181                                 feature colourscheme button</li>
182                         </ul>
183                         </li>
184                 </ul>
185                 </td>
186         </tr>
187         <tr>
188
189                 <td>
190                 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
191                 <em>30/4/2010</em></div>
192                 </td>
193                 <td><em>New Capabilities</em>
194                 <ul>
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> -->
209                 </ul>
210                 <em>Application</em>
211                 <ul>
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
218                         terms).</li>
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
224                         plots</li>
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
235                         annotation</li>
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>
239                         <ul>
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
243                                 line</li>
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>
247                         </ul>
248                         </li>
249                 </ul>
250                 <em>Applet</em>
251                 <ul>
252                         <li>Middle button resizes annotation row height</li>
253                         <li>New Parameters
254                         <ul>
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>
266                         </ul>
267                         </li>
268                         <li>Non-positional features displayed in sequence ID tooltip</li>
269                 </ul>
270                 <em>Other</em>
271                 <ul>
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
279                         settings.</li>
280                 </td>
281                 <td>
282                 <ul>
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
287                         tooltip).</li>
288                         <li>URL links generated for all feature links (bugfix)</li>
289                         <li>Added URL embedding instructions to features file
290                         documentation.</li>
291                         <li>Codons containing ambiguous nucleotides translated as 'X' in
292                         peptide product</li>
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
300                         re-imported)</li>
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>
304                         <li>Application:
305                         <ul>
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
314                                 sources</li>
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
318                                 time.</li>
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
322                                 projects.</li>
323                         </ul>
324                         </li>
325                 </ul>
326                 </td>
327
328         </tr>
329         <tr>
330                 <td>
331                 <div align="center"><strong>2.4.0.b2</strong><br>
332                 28/10/2009</div>
333                 </td>
334                 <td>
335                 <ul>
336                         <li>Experimental support for google analytics usage tracking.</li>
337                         <li>Jalview privacy settings (user preferences and docs).</li>
338                 </ul>
339                 </td>
340                 <td>
341                 <ul>
342                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
343                         <li>Exception when feature created from selection beyond length
344                         of sequence.</li>
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
349                         string searches</li>
350                         <li>Non-standard characters do not cause pairwise alignment to
351                         fail with exception</li>
352                 </ul>
353                 <em>Application Issues</em>
354                 <ul>
355                         <li>Sequences are now validated against EMBL database</li>
356                         <li>Sequence fetcher fetches multiple records for all data
357                         sources</li>
358                 </ul>
359                 <em>InstallAnywhere Issues</em>
360                 <ul>
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>
365                 </ul>
366                 </td>
367         </tr>
368         <tr>
369                 <td>
370
371                 <div align="center"><strong>2.4</strong><br>
372                 27/8/2008</div>
373                 </td>
374                 <td><em>User Interface</em>
375                 <ul>
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
381                         'clear' button</li>
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
387                         sequence</li>
388                 </ul>
389                 <em>Web Services and URL fetching</em>
390                 <ul>
391                         <li>JPred3 web service</li>
392                         <li>Prototype sequence search client (no public services
393                         available yet)</li>
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>
398                 </ul>
399                 <em>Sequence Database Connectivity</em>
400                 <ul>
401                         <li>Retrieval of cross-referenced sequences from other databases
402                         </li>
403                         <li>Generalised database reference retrieval and validation to
404                         all fetchable databases</li>
405                         <li>Fetch sequences from DAS sources supporting the sequence
406                         command</li>
407                 </ul>
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>
415                 </ul>
416                 <em>VAMSAS Client capabilities (Experimental)</em>
417                 <ul>
418                         <li>treenode binding for VAMSAS tree exchange</li>
419                         <li>local editing and update of sequences in VAMSAS alignments
420                         (experimental)</li>
421                         <li>Create new or select existing session to join</li>
422                         <li>load and save of vamsas documents</li>
423                 </ul>
424                 <em>Application command line</em>
425                 <ul>
426                         <li>-tree parameter to open trees (introduced for passing from
427                         applet)</li>
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>
434                 </ul>
435                 <em>Applet-Application data exchange</em>
436                 <ul>
437                         <li>Trees passed as applet parameters can be passed to
438                         application (when using &quot;View in full application&quot;)</li>
439                 </ul>
440                 <em>Applet Parameters</em>
441                 <ul>
442                         <li>feature group display control parameter</li>
443                         <li>debug parameter</li>
444                         <li>showbutton parameter</li>
445                 </ul>
446                 <em>Applet API methods</em>
447                 <ul>
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>
452                 </ul>
453                 <em>New Jalview distribution features</em>
454                 <ul>
455                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
456                         <li>RELEASE file gives build properties for the latest Jalview
457                         release.</li>
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>
466                 </ul>
467
468                 </td>
469                 <td>
470                 <ul>
471                         <li>selected region output includes visible annotations (for
472                         certain formats)</li>
473                         <li>edit label/displaychar contains existing label/char for
474                         editing</li>
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
479                         comments</li>
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
490                         parsing fails.</li>
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
498                         is edited</li>
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
505                         list</li>
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
518                         2008</li>
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
538                         client</li>
539                         <li>Re-instated Full AMSA support and .amsa file association</li>
540                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
541                         sequences</li>
542                 </ul>
543                 </td>
544         </tr>
545         <tr>
546                 <td>
547                 <div align="center"><strong>2.3</strong><br>
548                 9/5/07</div>
549                 </td>
550                 <td>
551                 <ul>
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>
563                 </ul>
564                 </td>
565                 <td>
566                 <ul>
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>
578                 </ul>
579                 </td>
580
581         </tr>
582         <tr>
583                 <td>
584                 <div align="center"><strong>2.2.1</strong><br>
585                 12/2/07</div>
586                 </td>
587                 <td>
588                 <ul>
589                         <li>Non standard characters can be read and displayed
590                         <li>Annotations/Features can be imported/exported to the applet
591                         via textbox
592                         <li>Applet allows editing of sequence/annotation/group name
593                         &amp; description
594                         <li>Preference setting to display sequence name in italics
595                         <li>Annotation file format extended to allow Sequence_groups to
596                         be defined
597                         <li>Default opening of alignment overview panel can be specified
598                         in preferences
599                         <li>PDB residue numbering annotation added to associated
600                         sequences
601                 </ul>
602                 </td>
603                 <td>
604                 <ul>
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
608                 </ul>
609                 </td>
610         </tr>
611         <tr>
612                 <td>
613                 <div align="center"><strong>2.2</strong><br>
614                 27/11/06</div>
615                 </td>
616                 <td>
617                 <ul>
618                         <li>Multiple views on alignment
619                         <li>Sequence feature editing
620                         <li>&quot;Reload&quot; alignment
621                         <li>&quot;Save&quot; to current filename
622                         <li>Background dependent text colour
623                         <li>Right align sequence ids
624                         <li>User-defined lower case residue colours
625                         <li>Format Menu
626                         <li>Select Menu
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'
633                 </ul>
634                 </td>
635                 <td>
636                 <ul>
637                         <li>New memory efficient Undo/Redo System
638                         <li>Optimised symbol lookups and conservation/consensus
639                         calculations
640                         <li>Region Conservation/Consensus recalculated after edits
641                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
642                         alignment)
643                         <li>Slowed DAS Feature Fetching for increased robustness.
644                         <li>Made angle brackets in ASCII feature descriptions display
645                         correctly
646                         <li>Re-instated Zoom function for PCA
647                         <li>Sequence descriptions conserved in web service analysis
648                         results
649                         <li>Uniprot ID discoverer uses any word separated by &#8739;
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.
653                 </ul>
654                 </td>
655         </tr>
656         <tr>
657                 <td>
658                 <div align="center"><strong>2.1.1</strong><br>
659                 12/9/06</div>
660                 </td>
661                 <td>
662                 <ul>
663                         <li>Copy consensus sequence to clipboard</li>
664                 </ul>
665                 </td>
666                 <td>
667                 <ul>
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>
674                 </ul>
675                 </td>
676         </tr>
677         <tr>
678                 <td>
679                 <div align="center"><strong>2.1</strong><br>
680                 22/8/06</div>
681                 </td>
682                 <td>
683                 <ul>
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 &quot;sequence<em>x</em>&quot;</li>
696                 </ul>
697                 </td>
698                 <td>
699                 <ul>
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>
703                 </ul>
704                 </td>
705         </tr>
706         <tr>
707                 <td>
708                 <div align="center"><strong>2.08.1</strong><br>
709                 2/5/06</div>
710                 </td>
711                 <td>
712                 <ul>
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>
717                 </ul>
718                 </td>
719                 <td>
720                 <ul>
721                         <li>Annotation Panel displays complete JNet results</li>
722                 </ul>
723                 </td>
724         </tr>
725         <tr>
726                 <td>
727                 <div align="center"><strong>2.08b</strong><br>
728                 18/4/06</div>
729                 </td>
730                 <td>&nbsp;</td>
731                 <td>
732                 <ul>
733                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
734                         <li>Righthand label on wrapped alignments shows correct value</li>
735                 </ul>
736                 </td>
737         </tr>
738         <tr>
739                 <td>
740                 <div align="center"><strong>2.08</strong><br>
741                 10/4/06</div>
742                 </td>
743                 <td>
744                 <ul>
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>
753                 </ul>
754                 </td>
755                 <td>
756                 <ul>
757                         <li>Drag &amp; Drop fixed on Linux</li>
758                         <li>Jalview Archive file faster to load/save, sequence
759                         descriptions saved.</li>
760                 </ul>
761                 </td>
762         </tr>
763         <tr>
764                 <td>
765                 <div align="center"><strong>2.07</strong><br>
766                 12/12/05</div>
767                 </td>
768                 <td>
769                 <ul>
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
773                         file output</li>
774                         <li>Sequence Fetcher WSDBFetch@EBI</li>
775                         <li>Applet can read feature files, PDB files and can be used for
776                         HTML form input</li>
777                 </ul>
778                 </td>
779                 <td>
780                 <ul>
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>
784                 </ul>
785                 </td>
786         </tr>
787         <tr>
788                 <td>
789                 <div align="center"><strong>2.06</strong><br>
790                 28/9/05</div>
791                 </td>
792                 <td>
793                 <ul>
794                         <li>View annotations in wrapped mode</li>
795                         <li>More options for PCA viewer</li>
796                 </ul>
797                 </td>
798                 <td>
799                 <ul>
800                         <li>GUI bugs resolved</li>
801                         <li>Runs with -nodisplay from command line</li>
802                 </ul>
803                 </td>
804         </tr>
805         <tr>
806                 <td height="63">
807                 <div align="center"><strong>2.05b</strong><br>
808                 15/9/05</div>
809                 </td>
810                 <td>
811                 <ul>
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>
815                 </ul>
816                 </td>
817                 <td>
818                 <ul>
819                         <li>Known OutOfMemory errors give warning message</li>
820                         <li>Overview window calculated more efficiently</li>
821                         <li>Several GUI bugs resolved</li>
822                 </ul>
823                 </td>
824         </tr>
825         <tr>
826                 <td>
827                 <div align="center"><strong>2.05</strong><br>
828                 30/8/05</div>
829                 </td>
830                 <td>
831                 <ul>
832                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
833                 </ul>
834                 </td>
835                 <td>
836                 <ul>
837                         <li>Several GUI bugs resolved</li>
838                 </ul>
839                 </td>
840         </tr>
841         <tr>
842                 <td>
843                 <div align="center"><strong>2.04</strong><br>
844                 24/8/05</div>
845                 </td>
846                 <td>
847                 <ul>
848                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
849                 </ul>
850                 </td>
851                 <td>
852                 <ul>
853                         <li>Improved JPred client reliability</li>
854                         <li>Improved loading of Jalview files</li>
855                 </ul>
856                 </td>
857         </tr>
858         <tr>
859                 <td>
860                 <div align="center"><strong>2.03</strong><br>
861                 18/8/05</div>
862                 </td>
863                 <td>
864                 <ul>
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
868                         Colour Menu</li>
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>
873                 </ul>
874                 </td>
875                 <td>
876                 <ul>
877                         <li>InstallAnywhere download for Sparc Solaris</li>
878                 </ul>
879                 </td>
880         </tr>
881         <tr>
882                 <td>
883                 <div align="center"><strong>2.02</strong><br>
884                 18/7/05</div>
885                 </td>
886                 <td>&nbsp;</td>
887                 <td>
888                 <ul>
889                         <li>Copy &amp; Paste order of sequences maintains alignment
890                         order.</li>
891                 </ul>
892                 </td>
893         </tr>
894         <tr>
895                 <td>
896                 <div align="center"><strong>2.01</strong><br>
897                 12/7/05</div>
898                 </td>
899                 <td>
900                 <ul>
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
904                         annotations.</li>
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>
908                 </ul>
909                 </td>
910                 <td>
911                 <ul>
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>
918                         </li>
919                 </ul>
920                 </td>
921         </tr>
922         <tr>
923                 <td>
924                 <div align="center"><strong>2.0</strong><br>
925                 20/6/05</div>
926                 </td>
927                 <td>
928                 <ul>
929                         <li>New codebase</li>
930                 </ul>
931                 </td>
932                 <td>&nbsp;</td>
933         </tr>
934 </table>
935 <p>&nbsp;</p>
936 </body>
937 </html>