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2 <!--
3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
4  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
5  * 
6  * This file is part of Jalview.
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8  * Jalview is free software: you can redistribute it and/or
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10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11  * 
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 
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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">
39                                         <strong><a name="Jalview2.7">2.7</a>
40                                         </strong><br> <em>27/09/2011</em>
41                                 </div></td>
42                         <td><em>Application</em>
43                                 <ul>
44                                         <li>Jalview Desktop News Reader</li>
45                                         <li>Tweaked default layout of web services menu</li>
46                                         <li>View/alignment association menu to enable user to easily
47                                                 specify which alignment a multi-structure view takes its
48                                                 colours/correspondences from</li>
49                                         <li>Allow properties file location to be specified as URL </li>
50                                                 <li>Extend jalview project to preserve associations between
51                                                         many alignment views and a single Jmol display</li>
52                                                 <li>Store annotation row height in jalview project file</li>
53                                                 <li>Annotation row column label formatting attributes stored
54                                                         in project file</li>
55                                                 <li>Annotation row order for auto-calculated annotation rows
56                                                         preserved in jalview project file</li>
57                                                 <li>Visual progress indication when Jalview state is saved
58                                                         using Desktop window menu</li>
59                                                 <li>Visual indication that command line arguments are still
60                                                         being processed</li>
61                                                 <li>Groovy script execution from URL</li>
62                                                 <li>Colour by annotation default min and max colours in
63                                                         preferences</li>
64                                                 <li>Automatically associate PDB files dragged onto an
65                                                         alignment with sequences that have high similarity and matching
66                                                         IDs</li>
67                                                 <li>Update JGoogleAnalytics to latest release (0.3)</li>
68                                                 <li>&#39;view structures&#39; option to open many structures
69                                                         in same window</li>
70                                                 <li>Sort associated views menu option for tree panel</li>
71                                                 <li>Group all JABA and non-JABA services for a particular
72                                                         analysis function in its own submenu</li>
73                                 </ul> <em>Applet</em>
74                         <ul>
75                                         <li>Userdefined and autogenerated annotation rows for groups</li>
76                                         <li>Adjustment of alignment annotation pane height</li>
77                                         <li>Annotation scrollbar for annotation panel</li>
78                                         <li>Drag to reorder annotation rows in annotation panel</li>
79                                         <li>&#39;automaticScrolling&#39; parameter</li>
80                                         <li>Allow sequences with partial ID string matches to be
81                                                 annotated from GFF/jalview features files</li>
82                                         <li>Sequence logo annotation row in applet</li>
83                                         <li>Absolute paths relative to host server in applet
84                                                 parameters are treated as such</li>
85                                         <li>New in the JalviewLite javascript API:
86                                                 <ul>
87                                                         <li>JalviewLite.js javascript library</li>
88                                                         <li>Javascript callbacks for
89                                                                 <ul>
90                                                                         <li>Applet initialisation</li>
91                                                                         <li>Sequence/alignment mouse-overs and selections</li>
92                                                                 </ul>
93                                                         </li>
94                                                         <li>scrollTo row and column alignment scrolling functions</li>
95                                                         <li>Select sequence/alignment regions from javascript</li>
96                                                         <li>javascript structure viewer harness to pass messages
97                                                                 between Jmol and Jalview when running as distinct applets</li>
98                                                         <li>sortBy method</li>
99                                                         <li>Set of applet and application examples shipped with
100                                                                 documentation</li>
101                                                         <li>New example to demonstrate jalviewLite and Jmol
102                                                                 javascript message exchange</li>
103                                                 </ul>
104                                 </ul> <em>General</em>
105                                 <ul>
106                                         <li>Enable Jmol displays to be associated with multiple
107                                                 multiple alignments</li>
108                                         <li>Option to automatically sort alignment with new tree</li>
109                                         <li>User configurable link to enable redirects to a
110                                                 www.jalview.org mirror</li>
111                                         <li>Jmol colours option for Jmol displays</li>
112                                         <li>Configurable newline string when writing alignment and
113                                                 other flat files</li>
114                                         <li>Allow alignment annotation description lines to contain
115                                                 html tags</li>
116                                 </ul> <em>Documentation and Development</em>
117                                 <ul>
118                                         <li>Add groovy test harness for bulk load testing to examples
119                                         </li>
120                                         <li>Groovy script to load and align a set of sequences using a
121                                                 web service before displaying the result in the Jalview desktop</li>
122                                         <li>Restructured javascript and applet api documentation</li>
123                                         <li>Ant target to publish example html files with applet archive</li>
124                                         <li>Netbeans project for building jalview from source</li>
125                                         <li>ant task to create online javadoc for jalview source</li>
126                                 </ul></td>
127                         <td><em>Application</em>
128                                 <ul>
129                                         <li>User defined colourscheme throws exception when current
130                                                 built in colourscheme is saved as new scheme</li>
131                                         <li>AlignFrame-&gt;Save in application pops up save dialog for
132                                                 valid filename/format</li>
133                                         <li>Cannot view associated structure for Uniprot sequence</li>
134                                         <li>PDB file association breaks for Uniprot sequence P37173</li>
135                                         <li>Associate PDB from file dialog does not tell you which
136                                                 sequence is to be associated with the file</li>
137                                         <li>Find All raises null pointer exception when query only
138                                                 matches sequence IDs</li>
139                                         <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
140                                         <li>Jalview project with Jmol views created with Jalview 2.4
141                                                 cannot be loaded</li>
142                                         <li>Filetype associations not installed for webstart launch</li>
143                                         <li>Two or more chains in a single PDB file associated with
144                                                 sequences in different alignments do not get coloured by their
145                                                 associated sequence</li>
146                                         <li>Visibility status of autocalculated annotation row not
147                                                 preserved when project is loaded</li>
148                                         <li>Annotation row height and visibility attributes not stored
149                                                 in jalview project</li>
150                                         <li>Tree bootstraps are not preserved when saved as a jalview
151                                                 project</li>
152                                         <li>Envision2 workflow tooltips are corrupted</li>
153                                         <li>Enabling show group conservation also enables colour by
154                                                 conservation</li>
155                                         <li>Duplicate group associated conservation or consensus
156                                                 created on new view</li>
157                                         <li>Annotation scrollbar not displayed after &#39;show all
158                                                 hidden annotation rows&#39; option selected</li>
159                                         <li>Alignment quality not updated after alignment annotation
160                                                 row is hidden then shown</li>
161                                         <li>Preserve colouring of structures coloured by sequences in pre
162                                                 jalview 2.7 projects</li>
163                                         <li>Web service job parameter dialog is not laid out properly
164                                         </li>
165                                         <li>Web services menu not refreshed after &#39;reset
166                                                 services&#39; button is pressed in preferences</li>
167                                         <li>Annotation off by one in jalview v2_3 example project</li>
168                                         <li>Structures imported from file and saved in project get
169                                                 name like jalview_pdb1234.txt when reloaded</li>
170                                         <li>Jalview does not always retrieve progress of a JABAWS job
171                                                 execution in full once it is complete</li>
172                                 </ul> <em>Applet</em>
173                                 <ul>
174                                         <li>Alignment height set incorrectly when lots of annotation
175                                                 rows are displayed</li>
176                                         <li>Relative URLs in feature HTML text not resolved to
177                                                 codebase</li>
178                                         <li>View follows highlighting does not work for positions in
179                                                 sequences</li>
180                                         <li>&lt;= shown as = in tooltip</li>
181                                         <li>Export features raises exception when no features exist</li>
182                                         <li>Separator string used for serialising lists of IDs for
183                                                 javascript api is modified when separator string provided as
184                                                 parameter</li>
185                                         <li>Null pointer exception when selecting tree leaves for
186                                                 alignment with no existing selection</li>
187                                         <li>Relative URLs for datasources assumed to be relative to
188                                                 applet&#39;s codebase</li>
189                                         <li>Status bar not updated after finished searching and search
190                                                 wraps around to first result</li>
191                                         <li>StructureSelectionManager instance shared between several
192                                                 jalview applets causes race conditions and memory leaks</li>
193                                         <li>Hover tooltip and mouseover of position on structure not
194                                                 sent from Jmol in applet</li>
195                                         <li>Certain sequences of javascript method calls to applet API
196                                                 fatally hang browser</li>
197                                 </ul> <em>General</em>
198                                 <ul>
199                                         <li>View follows structure mouseover scrolls beyond position
200                                                 with wrapped view and hidden regions</li>
201                                         <li>Find sequence position moves to wrong residue with/without
202                                                 hidden columns</li>
203                                         <li>Sequence length given in alignment properties window is
204                                                 off by 1</li>
205                                         <li>InvalidNumberFormat exceptions thrown when trying to
206                                                 import PDB like structure files</li>
207                                         <li>Positional search results are only highlighted between
208                                                 user-supplied sequence start/end bounds</li>
209                                         <li>End attribute of sequence is not validated</li>
210                                         <li>Find dialog only finds first sequence containing a given
211                                                 sequence position</li>
212                                         <li>Sequence numbering not preserved in MSF alignment output</li>
213                                         <li>Jalview PDB file reader does not extract sequence from
214                                                 nucleotide chains correctly</li>
215                                         <li>Structure colours not updated when tree partition changed
216                                                 in alignment</li>
217                                         <li>Sequence associated secondary structure not correctly
218                                                 parsed in interleaved stockholm</li>
219                                         <li>Colour by annotation dialog does not restore current state
220                                         </li>
221                                         <li>Hiding (nearly) all sequences doesn&#39;t work properly</li>
222                                         <li>Sequences containing lowercase letters are not properly
223                                                 associated with their pdb files</li>
224                                 </ul> <em>Documentation and Development</em>
225                                 <ul>
226                                         <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
227                                                 tool</li>
228                                 </ul></td>
229                 </tr>
230                 <tr>
231                         <td>
232                                 <div align="center">
233                                         <strong><a name="Jalview2.6.1">2.6.1</a>
234                                         </strong><br> <em>15/11/2010</em>
235                                 </div></td>
236                         <td><em>Application</em>
237                                 <ul>
238                                         <li>New warning dialog when the Jalview Desktop cannot contact
239                                                 web services</li>
240                                         <li>JABA service parameters for a preset are shown in service
241                                                 job window</li>
242                                         <li>JABA Service menu entries reworded</li>
243                                 </ul></td>
244                         <td>
245                                 <ul>
246                                         <li>Modeller PIR IO broken - cannot correctly import a pir
247                                                 file emitted by jalview</li>
248                                         <li>Existing feature settings transferred to new alignment
249                                                 view created from cut'n'paste</li>
250                                         <li>Improved test for mixed amino/nucleotide chains when
251                                                 parsing PDB files</li>
252                                         <li>Consensus and conservation annotation rows occasionally
253                                                 become blank for all new windows</li>
254                                         <li>Exception raised when right clicking above sequences in
255                                                 wrapped view mode</li>
256                                 </ul> <em>Application</em>
257                                 <ul>
258                                         <li>multiple multiply aligned structure views cause cpu usage
259                                                 to hit 100% and computer to hang</li>
260                                         <li>Web Service parameter layout breaks for long user
261                                                 parameter names</li>
262                                         <li>Jaba service discovery hangs desktop if Jaba server is
263                                                 down</li>
264                                 </ul></td>
265                 </tr>
266                 <tr>
267                 <td>
268                 <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
269                 <em>26/9/2010</em></div>
270                 </td>
271                 <td><em>Application</em>
272                 <ul>
273                         <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
274                         <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
275                         <li>Web Services preference tab</li>
276                         <li>Analysis parameters dialog box and user defined preferences</li>
277                         <li>Improved speed and layout of Envision2 service menu</li>
278                         <li>Superpose structures using associated sequence alignment</li>
279                         <li>Export coordinates and projection as CSV from PCA viewer</li>
280                 </ul>
281                 <em>Applet</em>
282                 <ul>
283                         <li>enable javascript: execution by the applet via the link out
284                         mechanism</li>
285                 </ul>
286                 <em>Other</em>
287                 <ul>
288                         <li>Updated the Jmol Jalview interface to work with Jmol series
289                         12</li>
290                         <li>The Jalview Desktop and JalviewLite applet now require Java
291                         1.5</li>
292                         <li>Allow Jalview feature colour specification for GFF sequence
293                         annotation files</li>
294                         <li>New 'colour by label' keword in jalview feature file type
295                         colour specification</li>
296                         <li>New Jalview Desktop Groovy API method that allows a script
297                         to check if it being run in an interactive session or in a batch
298                         operation from the jalview command line</li>
299                 </ul>
300                 </td>
301                 <td>
302                 <ul>
303                         <li>clustalx colourscheme colours Ds preferentially when both
304                         D+E are present in over 50% of the column</li>
305                 </ul>
306
307                 <em>Application</em>
308                 <ul>
309                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
310                         selected Regions menu item</li>
311                         <li>sequence fetcher replaces ',' for ';' when the ',' is part
312                         of a valid accession ID</li>
313                         <li>fatal OOM if object retrieved by sequence fetcher runs out
314                         of memory</li>
315                         <li>unhandled Out of Memory Error when viewing pca analysis
316                         results</li>
317                         <li>InstallAnywhere builds fail to launch on OS X java 10.5
318                         update 4 (due to apple Java 1.6 update)</li>
319                         <li>Installanywhere Jalview silently fails to launch</li>
320                 </ul>
321                 <em>Applet</em>
322                 <ul>
323                         <li>Jalview.getFeatureGroups() raises an
324                         ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
325                 </ul>
326                 </td>
327         </tr>
328         <tr>
329                 <td>
330                 <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
331                 <em>14/6/2010</em></div>
332                 </td>
333                 <td></td>
334                 <td>
335                 <ul>
336                         <li>Alignment prettyprinter doesn't cope with long sequence IDs
337                         </li>
338                         <li>clustalx colourscheme colours Ds preferentially when both
339                         D+E are present in over 50% of the column</li>
340                         <li>nucleic acid structures retrieved from PDB do not import
341                         correctly</li>
342                         <li>More columns get selected than were clicked on when a number
343                         of columns are hidden</li>
344                         <li>annotation label popup menu not providing correct
345                         add/hide/show options when rows are hidden or none are present</li>
346                         <li>Stockholm format shown in list of readable formats, and
347                         parser copes better with alignments from RFAM.</li>
348                         <li>CSV output of consensus only includes the percentage of all
349                         symbols if sequence logo display is enabled</li>
350
351                 </ul>
352                 <em>Applet</em>
353                 <ul>
354                         <li>annotation panel disappears when annotation is
355                         hidden/removed</li>
356                 </ul>
357                 <em>Application</em>
358                 <ul>
359                         <li>Alignment view not redrawn properly when new alignment
360                         opened where annotation panel is visible but no annotations are
361                         present on alignment</li>
362                         <li>pasted region containing hidden columns is incorrectly
363                         displayed in new alignment window</li>
364                         <li>Jalview slow to complete operations when stdout is flooded
365                         (fix is to close the Jalview console)</li>
366                         <li>typo in AlignmentFrame-&gt;View-&gt;Hide-&gt;all but
367                         selected Rregions menu item.</li>
368                         <li>inconsistent group submenu and Format submenu entry 'Un' or
369                         'Non'conserved</li>
370                         <li>Sequence feature settings are being shared by multiple
371                         distinct alignments</li>
372                         <li>group annotation not recreated when tree partition is
373                         changed</li>
374                         <li>double click on group annotation to select sequences does
375                         not propagate to associated trees</li>
376                         <li>Mac OSX specific issues:
377                         <ul>
378                                 <li>exception raised when mouse clicked on desktop window
379                                 background</li>
380                                 <li>Desktop menu placed on menu bar and application name set
381                                 correctly</li>
382                                 <li>sequence feature settings not wide enough for the save
383                                 feature colourscheme button</li>
384                         </ul>
385                         </li>
386                 </ul>
387                 </td>
388         </tr>
389         <tr>
390
391                 <td>
392                 <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
393                 <em>30/4/2010</em></div>
394                 </td>
395                 <td><em>New Capabilities</em>
396                 <ul>
397                         <li>URL links generated from description line for
398                         regular-expression based URL links (applet and application)
399                         <li>Non-positional feature URL links are shown in link menu</li>
400                         <li>Linked viewing of nucleic acid sequences and structures</li>
401                         <li>Automatic Scrolling option in View menu to display the
402                         currently highlighted region of an alignment.</li>
403                         <li>Order an alignment by sequence length, or using the average
404                         score or total feature count for each sequence.</li>
405                         <li>Shading features by score or associated description</li>
406                         <li>Subdivide alignment and groups based on identity of selected
407                         subsequence (Make Groups from Selection).</li>
408                         <li>New hide/show options including Shift+Control+H to hide
409                         everything but the currently selected region.</li>
410                         <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
411                 </ul>
412                 <em>Application</em>
413                 <ul>
414                         <li>Fetch DB References capabilities and UI expanded to support
415                         retrieval from DAS sequence sources</li>
416                         <li>Local DAS Sequence sources can be added via the command line
417                         or via the Add local source dialog box.</li>
418                         <li>DAS Dbref and DbxRef feature types are parsed as database
419                         references and protein_name is parsed as description line (BioSapiens
420                         terms).</li>
421                         <li>Enable or disable non-positional feature and database
422                         references in sequence ID tooltip from View menu in application.</li>
423                         <!--                    <li>New hidden columns and rows and representatives capabilities
424                         in annotations file (in progress - not yet fully implemented)</li> -->
425                         <li>Group-associated consensus, sequence logos and conservation
426                         plots</li>
427                         <li>Symbol distributions for each column can be exported and
428                         visualized as sequence logos</li>
429                         <li>Optionally scale multi-character column labels to fit within
430                         each column of annotation row<!-- todo for applet --></li>
431                         <li>Optional automatic sort of associated alignment view when a
432                         new tree is opened.</li>
433                         <li>Jalview Java Console</li>
434                         <li>Better placement of desktop window when moving between
435                         different screens.</li>
436                         <li>New preference items for sequence ID tooltip and consensus
437                         annotation</li>
438                         <li>Client to submit sequences and IDs to <a
439                                 href="webServices/index.html#envision2">Envision2</a> Workflows</li>
440                         <li><em>Vamsas Capabilities</em>
441                         <ul>
442                                 <li>Improved VAMSAS synchronization (jalview archive used to
443                                 preserve views, structures, and tree display settings)</li>
444                                 <li>Import of vamsas documents from disk or URL via command
445                                 line</li>
446                                 <li>Sharing of selected regions between views and with other
447                                 VAMSAS applications (Experimental feature!)</li>
448                                 <li>Updated API to VAMSAS version 0.2</li>
449                         </ul>
450                         </li>
451                 </ul>
452                 <em>Applet</em>
453                 <ul>
454                         <li>Middle button resizes annotation row height</li>
455                         <li>New Parameters
456                         <ul>
457                                 <li>sortByTree (true/false) - automatically sort the associated
458                                 alignment view by the tree when a new tree is opened.</li>
459                                 <li>showTreeBootstraps (true/false) - show or hide branch
460                                 bootstraps (default is to show them if available)</li>
461                                 <li>showTreeDistances (true/false) - show or hide branch
462                                 lengths (default is to show them if available)</li>
463                                 <li>showUnlinkedTreeNodes (true/false) - indicate if
464                                 unassociated nodes should be highlighted in the tree view</li>
465                                 <li>heightScale and widthScale (1.0 or more) - increase the
466                                 height or width of a cell in the alignment grid relative to the
467                                 current font size.</li>
468                         </ul>
469                         </li>
470                         <li>Non-positional features displayed in sequence ID tooltip</li>
471                 </ul>
472                 <em>Other</em>
473                 <ul>
474                         <li>Features format: graduated colour definitions and
475                         specification of feature scores</li>
476                         <li>Alignment Annotations format: new keywords for group
477                         associated annotation (GROUP_REF) and annotation row display
478                         properties (ROW_PROPERTIES)</li>
479                         <li>XML formats extended to support graduated feature
480                         colourschemes, group associated annotation, and profile visualization
481                         settings.</li>
482                 </td>
483                 <td>
484                 <ul>
485                         <li>Source field in GFF files parsed as feature source rather
486                         than description</li>
487                         <li>Non-positional features are now included in sequence feature
488                         and gff files (controlled via non-positional feature visibility in
489                         tooltip).</li>
490                         <li>URL links generated for all feature links (bugfix)</li>
491                         <li>Added URL embedding instructions to features file
492                         documentation.</li>
493                         <li>Codons containing ambiguous nucleotides translated as 'X' in
494                         peptide product</li>
495                         <li>Match case switch in find dialog box works for both sequence
496                         ID and sequence string and query strings do not have to be in upper
497                         case to match case-insensitively.</li>
498                         <li>AMSA files only contain first column of multi-character
499                         column annotation labels</li>
500                         <li>Jalview Annotation File generation/parsing consistent with
501                         documentation (e.g. Stockholm annotation can be exported and
502                         re-imported)</li>
503                         <li>PDB files without embedded PDB IDs given a friendly name</li>
504                         <li>Find incrementally searches ID string matches as well as
505                         subsequence matches, and correctly reports total number of both.</li>
506                         <li>Application:
507                         <ul>
508                                 <li>Better handling of exceptions during sequence retrieval</li>
509                                 <li>Dasobert generated non-positional feature URL link text
510                                 excludes the start_end suffix</li>
511                                 <li>DAS feature and source retrieval buttons disabled when
512                                 fetch or registry operations in progress.</li>
513                                 <li>PDB files retrieved from URLs are cached properly</li>
514                                 <li>Sequence description lines properly shared via VAMSAS</li>
515                                 <li>Sequence fetcher fetches multiple records for all data
516                                 sources</li>
517                                 <li>Ensured that command line das feature retrieval completes
518                                 before alignment figures are generated.</li>
519                                 <li>Reduced time taken when opening file browser for first
520                                 time.</li>
521                                 <li>isAligned check prior to calculating tree, PCA or
522                                 submitting an MSA to JNet now excludes hidden sequences.</li>
523                                 <li>User defined group colours properly recovered from Jalview
524                                 projects.</li>
525                         </ul>
526                         </li>
527                 </ul>
528                 </td>
529
530         </tr>
531         <tr>
532                 <td>
533                 <div align="center"><strong>2.4.0.b2</strong><br>
534                 28/10/2009</div>
535                 </td>
536                 <td>
537                 <ul>
538                         <li>Experimental support for google analytics usage tracking.</li>
539                         <li>Jalview privacy settings (user preferences and docs).</li>
540                 </ul>
541                 </td>
542                 <td>
543                 <ul>
544                         <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
545                         <li>Exception when feature created from selection beyond length
546                         of sequence.</li>
547                         <li>Allow synthetic PDB files to be imported gracefully</li>
548                         <li>Sequence associated annotation rows associate with all
549                         sequences with a given id</li>
550                         <li>Find function matches case-insensitively for sequence ID
551                         string searches</li>
552                         <li>Non-standard characters do not cause pairwise alignment to
553                         fail with exception</li>
554                 </ul>
555                 <em>Application Issues</em>
556                 <ul>
557                         <li>Sequences are now validated against EMBL database</li>
558                         <li>Sequence fetcher fetches multiple records for all data
559                         sources</li>
560                 </ul>
561                 <em>InstallAnywhere Issues</em>
562                 <ul>
563                         <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
564                         installAnywhere mechanism)</li>
565                         <li>Command line launching of JARs from InstallAnywhere version
566                         (java class versioning error fixed)</li>
567                 </ul>
568                 </td>
569         </tr>
570         <tr>
571                 <td>
572
573                 <div align="center"><strong>2.4</strong><br>
574                 27/8/2008</div>
575                 </td>
576                 <td><em>User Interface</em>
577                 <ul>
578                         <li>Linked highlighting of codon and amino acid from translation
579                         and protein products</li>
580                         <li>Linked highlighting of structure associated with residue
581                         mapping to codon position</li>
582                         <li>Sequence Fetcher provides example accession numbers and
583                         'clear' button</li>
584                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
585                         <li>Extract score function to parse whitespace separated numeric
586                         data in description line</li>
587                         <li>Column labels in alignment annotation can be centred.</li>
588                         <li>Tooltip for sequence associated annotation give name of
589                         sequence</li>
590                 </ul>
591                 <em>Web Services and URL fetching</em>
592                 <ul>
593                         <li>JPred3 web service</li>
594                         <li>Prototype sequence search client (no public services
595                         available yet)</li>
596                         <li>Fetch either seed alignment or full alignment from PFAM</li>
597                         <li>URL Links created for matching database cross references as
598                         well as sequence ID</li>
599                         <li>URL Links can be created using regular-expressions</li>
600                 </ul>
601                 <em>Sequence Database Connectivity</em>
602                 <ul>
603                         <li>Retrieval of cross-referenced sequences from other databases
604                         </li>
605                         <li>Generalised database reference retrieval and validation to
606                         all fetchable databases</li>
607                         <li>Fetch sequences from DAS sources supporting the sequence
608                         command</li>
609                 </ul>
610                 <em>Import and Export</em>
611                 <li>export annotation rows as CSV for spreadsheet import</li>
612                 <li>Jalview projects record alignment dataset associations, EMBL
613                 products, and cDNA sequence mappings</li>
614                 <li>Sequence Group colour can be specified in Annotation File</li>
615                 <li>Ad-hoc colouring of group in Annotation File using RGB
616                 triplet as name of colourscheme</li>
617                 </ul>
618                 <em>VAMSAS Client capabilities (Experimental)</em>
619                 <ul>
620                         <li>treenode binding for VAMSAS tree exchange</li>
621                         <li>local editing and update of sequences in VAMSAS alignments
622                         (experimental)</li>
623                         <li>Create new or select existing session to join</li>
624                         <li>load and save of vamsas documents</li>
625                 </ul>
626                 <em>Application command line</em>
627                 <ul>
628                         <li>-tree parameter to open trees (introduced for passing from
629                         applet)</li>
630                         <li>-fetchfrom command line argument to specify nicknames of DAS
631                         servers to query for alignment features</li>
632                         <li>-dasserver command line argument to add new servers that are
633                         also automatically queried for features</li>
634                         <li>-groovy command line argument executes a given groovy script
635                         after all input data has been loaded and parsed</li>
636                 </ul>
637                 <em>Applet-Application data exchange</em>
638                 <ul>
639                         <li>Trees passed as applet parameters can be passed to
640                         application (when using &quot;View in full application&quot;)</li>
641                 </ul>
642                 <em>Applet Parameters</em>
643                 <ul>
644                         <li>feature group display control parameter</li>
645                         <li>debug parameter</li>
646                         <li>showbutton parameter</li>
647                 </ul>
648                 <em>Applet API methods</em>
649                 <ul>
650                         <li>newView public method</li>
651                         <li>Window (current view) specific get/set public methods</li>
652                         <li>Feature display control methods</li>
653                         <li>get list of currently selected sequences</li>
654                 </ul>
655                 <em>New Jalview distribution features</em>
656                 <ul>
657                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
658                         <li>RELEASE file gives build properties for the latest Jalview
659                         release.</li>
660                         <li>Java 1.1 Applet build made easier and donotobfuscate
661                         property controls execution of obfuscator</li>
662                         <li>Build target for generating source distribution</li>
663                         <li>Debug flag for javacc</li>
664                         <li>.jalview_properties file is documented (slightly) in
665                         jalview.bin.Cache</li>
666                         <li>Continuous Build Integration for stable and development
667                         version of Application, Applet and source distribution</li>
668                 </ul>
669
670                 </td>
671                 <td>
672                 <ul>
673                         <li>selected region output includes visible annotations (for
674                         certain formats)</li>
675                         <li>edit label/displaychar contains existing label/char for
676                         editing</li>
677                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
678                         <li>shorter peptide product names from EMBL records</li>
679                         <li>Newick string generator makes compact representations</li>
680                         <li>bootstrap values parsed correctly for tree files with
681                         comments</li>
682                         <li>pathological filechooser bug avoided by not allowing
683                         filenames containing a ':'</li>
684                         <li>Fixed exception when parsing GFF files containing global
685                         sequence features</li>
686                         <li>Alignment datasets are finalized only when number of
687                         references from alignment sequences goes to zero</li>
688                         <li>Close of tree branch colour box without colour selection
689                         causes cascading exceptions</li>
690                         <li>occasional negative imgwidth exceptions</li>
691                         <li>better reporting of non-fatal warnings to user when file
692                         parsing fails.</li>
693                         <li>Save works when Jalview project is default format</li>
694                         <li>Save as dialog opened if current alignment format is not a
695                         valid output format</li>
696                         <li>Uniprot canonical names introduced for both das and vamsas</li>
697                         <li>Histidine should be midblue (not pink!) in Zappo</li>
698                         <li>error messages passed up and output when data read fails</li>
699                         <li>edit undo recovers previous dataset sequence when sequence
700                         is edited</li>
701                         <li>allow PDB files without pdb ID HEADER lines (like those
702                         generated by MODELLER) to be read in properly</li>
703                         <li>allow reading of JPred concise files as a normal filetype</li>
704                         <li>Stockholm annotation parsing and alignment properties import
705                         fixed for PFAM records</li>
706                         <li>Structure view windows have correct name in Desktop window
707                         list</li>
708                         <li>annotation consisting of sequence associated scores can be
709                         read and written correctly to annotation file</li>
710                         <li>Aligned cDNA translation to aligned peptide works correctly</li>
711                         <li>Fixed display of hidden sequence markers and non-italic font
712                         for representatives in Applet</li>
713                         <li>Applet Menus are always embedded in applet window on Macs.</li>
714                         <li>Newly shown features appear at top of stack (in Applet)</li>
715                         <li>Annotations added via parameter not drawn properly due to
716                         null pointer exceptions</li>
717                         <li>Secondary structure lines are drawn starting from first
718                         column of alignment</li>
719                         <li>Uniprot XML import updated for new schema release in July
720                         2008</li>
721                         <li>Sequence feature to sequence ID match for Features file is
722                         case-insensitive</li>
723                         <li>Sequence features read from Features file appended to all
724                         sequences with matching IDs</li>
725                         <li>PDB structure coloured correctly for associated views
726                         containing a sub-sequence</li>
727                         <li>PDB files can be retrieved by applet from Jar files</li>
728                         <li>feature and annotation file applet parameters referring to
729                         different directories are retrieved correctly</li>
730                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
731                         <li>Fixed application hang whilst waiting for splash-screen
732                         version check to complete</li>
733                         <li>Applet properly URLencodes input parameter values when
734                         passing them to the launchApp service</li>
735                         <li>display name and local features preserved in results
736                         retrieved from web service</li>
737                         <li>Visual delay indication for sequence retrieval and sequence
738                         fetcher initialisation</li>
739                         <li>updated Application to use DAS 1.53e version of dasobert DAS
740                         client</li>
741                         <li>Re-instated Full AMSA support and .amsa file association</li>
742                         <li>Fixed parsing of JNet Concise annotation <em>sans</em>
743                         sequences</li>
744                 </ul>
745                 </td>
746         </tr>
747         <tr>
748                 <td>
749                 <div align="center"><strong>2.3</strong><br>
750                 9/5/07</div>
751                 </td>
752                 <td>
753                 <ul>
754                         <li>Jmol 11.0.2 integration</li>
755                         <li>PDB views stored in Jalview XML files</li>
756                         <li>Slide sequences</li>
757                         <li>Edit sequence in place</li>
758                         <li>EMBL CDS features</li>
759                         <li>DAS Feature mapping</li>
760                         <li>Feature ordering</li>
761                         <li>Alignment Properties</li>
762                         <li>Annotation Scores</li>
763                         <li>Sort by scores</li>
764                         <li>Feature/annotation editing in applet</li>
765                 </ul>
766                 </td>
767                 <td>
768                 <ul>
769                         <li>Headless state operation in 2.2.1</li>
770                         <li>Incorrect and unstable DNA pairwise alignment</li>
771                         <li>Cut and paste of sequences with annotation</li>
772                         <li>Feature group display state in XML</li>
773                         <li>Feature ordering in XML</li>
774                         <li>blc file iteration selection using filename # suffix</li>
775                         <li>Stockholm alignment properties</li>
776                         <li>Stockhom alignment secondary structure annotation</li>
777                         <li>2.2.1 applet had no feature transparency</li>
778                         <li>Number pad keys can be used in cursor mode</li>
779                         <li>Structure Viewer mirror image resolved</li>
780                 </ul>
781                 </td>
782
783         </tr>
784         <tr>
785                 <td>
786                 <div align="center"><strong>2.2.1</strong><br>
787                 12/2/07</div>
788                 </td>
789                 <td>
790                 <ul>
791                         <li>Non standard characters can be read and displayed
792                         <li>Annotations/Features can be imported/exported to the applet
793                         via textbox
794                         <li>Applet allows editing of sequence/annotation/group name
795                         &amp; description
796                         <li>Preference setting to display sequence name in italics
797                         <li>Annotation file format extended to allow Sequence_groups to
798                         be defined
799                         <li>Default opening of alignment overview panel can be specified
800                         in preferences
801                         <li>PDB residue numbering annotation added to associated
802                         sequences
803                 </ul>
804                 </td>
805                 <td>
806                 <ul>
807                         <li>Applet crash under certain Linux OS with Java 1.6 installed
808                         <li>Annotation file export / import bugs fixed
809                         <li>PNG / EPS image output bugs fixed
810                 </ul>
811                 </td>
812         </tr>
813         <tr>
814                 <td>
815                 <div align="center"><strong>2.2</strong><br>
816                 27/11/06</div>
817                 </td>
818                 <td>
819                 <ul>
820                         <li>Multiple views on alignment
821                         <li>Sequence feature editing
822                         <li>&quot;Reload&quot; alignment
823                         <li>&quot;Save&quot; to current filename
824                         <li>Background dependent text colour
825                         <li>Right align sequence ids
826                         <li>User-defined lower case residue colours
827                         <li>Format Menu
828                         <li>Select Menu
829                         <li>Menu item accelerator keys
830                         <li>Control-V pastes to current alignment
831                         <li>Cancel button for DAS Feature Fetching
832                         <li>PCA and PDB Viewers zoom via mouse roller
833                         <li>User-defined sub-tree colours and sub-tree selection
834                         <li>'New Window' button on the 'Output to Text box'
835                 </ul>
836                 </td>
837                 <td>
838                 <ul>
839                         <li>New memory efficient Undo/Redo System
840                         <li>Optimised symbol lookups and conservation/consensus
841                         calculations
842                         <li>Region Conservation/Consensus recalculated after edits
843                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
844                         alignment)
845                         <li>Slowed DAS Feature Fetching for increased robustness.
846                         <li>Made angle brackets in ASCII feature descriptions display
847                         correctly
848                         <li>Re-instated Zoom function for PCA
849                         <li>Sequence descriptions conserved in web service analysis
850                         results
851                         <li>Uniprot ID discoverer uses any word separated by &#8739;
852                         <li>WsDbFetch query/result association resolved
853                         <li>Tree leaf to sequence mapping improved
854                         <li>Smooth fonts switch moved to FontChooser dialog box.
855                 </ul>
856                 </td>
857         </tr>
858         <tr>
859                 <td>
860                 <div align="center"><strong>2.1.1</strong><br>
861                 12/9/06</div>
862                 </td>
863                 <td>
864                 <ul>
865                         <li>Copy consensus sequence to clipboard</li>
866                 </ul>
867                 </td>
868                 <td>
869                 <ul>
870                         <li>Image output - rightmost residues are rendered if sequence
871                         id panel has been resized</li>
872                         <li>Image output - all offscreen group boundaries are rendered</li>
873                         <li>Annotation files with sequence references - all elements in
874                         file are relative to sequence position</li>
875                         <li>Mac Applet users can use Alt key for group editing</li>
876                 </ul>
877                 </td>
878         </tr>
879         <tr>
880                 <td>
881                 <div align="center"><strong>2.1</strong><br>
882                 22/8/06</div>
883                 </td>
884                 <td>
885                 <ul>
886                         <li>MAFFT Multiple Alignment in default Web Service list</li>
887                         <li>DAS Feature fetching</li>
888                         <li>Hide sequences and columns</li>
889                         <li>Export Annotations and Features</li>
890                         <li>GFF file reading / writing</li>
891                         <li>Associate structures with sequences from local PDB files</li>
892                         <li>Add sequences to exisiting alignment</li>
893                         <li>Recently opened files / URL lists</li>
894                         <li>Applet can launch the full application</li>
895                         <li>Applet has transparency for features (Java 1.2 required)</li>
896                         <li>Applet has user defined colours parameter</li>
897                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
898                 </ul>
899                 </td>
900                 <td>
901                 <ul>
902                         <li>Redundancy Panel reinstalled in the Applet</li>
903                         <li>Monospaced font - EPS / rescaling bug fixed</li>
904                         <li>Annotation files with sequence references bug fixed</li>
905                 </ul>
906                 </td>
907         </tr>
908         <tr>
909                 <td>
910                 <div align="center"><strong>2.08.1</strong><br>
911                 2/5/06</div>
912                 </td>
913                 <td>
914                 <ul>
915                         <li>Change case of selected region from Popup menu</li>
916                         <li>Choose to match case when searching</li>
917                         <li>Middle mouse button and mouse movement can compress / expand
918                         the visible width and height of the alignment</li>
919                 </ul>
920                 </td>
921                 <td>
922                 <ul>
923                         <li>Annotation Panel displays complete JNet results</li>
924                 </ul>
925                 </td>
926         </tr>
927         <tr>
928                 <td>
929                 <div align="center"><strong>2.08b</strong><br>
930                 18/4/06</div>
931                 </td>
932                 <td>&nbsp;</td>
933                 <td>
934                 <ul>
935                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
936                         <li>Righthand label on wrapped alignments shows correct value</li>
937                 </ul>
938                 </td>
939         </tr>
940         <tr>
941                 <td>
942                 <div align="center"><strong>2.08</strong><br>
943                 10/4/06</div>
944                 </td>
945                 <td>
946                 <ul>
947                         <li>Editing can be locked to the selection area</li>
948                         <li>Keyboard editing</li>
949                         <li>Create sequence features from searches</li>
950                         <li>Precalculated annotations can be loaded onto alignments</li>
951                         <li>Features file allows grouping of features</li>
952                         <li>Annotation Colouring scheme added</li>
953                         <li>Smooth fonts off by default - Faster rendering</li>
954                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
955                 </ul>
956                 </td>
957                 <td>
958                 <ul>
959                         <li>Drag &amp; Drop fixed on Linux</li>
960                         <li>Jalview Archive file faster to load/save, sequence
961                         descriptions saved.</li>
962                 </ul>
963                 </td>
964         </tr>
965         <tr>
966                 <td>
967                 <div align="center"><strong>2.07</strong><br>
968                 12/12/05</div>
969                 </td>
970                 <td>
971                 <ul>
972                         <li>PDB Structure Viewer enhanced</li>
973                         <li>Sequence Feature retrieval and display enhanced</li>
974                         <li>Choose to output sequence start-end after sequence name for
975                         file output</li>
976                         <li>Sequence Fetcher WSDBFetch@EBI</li>
977                         <li>Applet can read feature files, PDB files and can be used for
978                         HTML form input</li>
979                 </ul>
980                 </td>
981                 <td>
982                 <ul>
983                         <li>HTML output writes groups and features</li>
984                         <li>Group editing is Control and mouse click</li>
985                         <li>File IO bugs</li>
986                 </ul>
987                 </td>
988         </tr>
989         <tr>
990                 <td>
991                 <div align="center"><strong>2.06</strong><br>
992                 28/9/05</div>
993                 </td>
994                 <td>
995                 <ul>
996                         <li>View annotations in wrapped mode</li>
997                         <li>More options for PCA viewer</li>
998                 </ul>
999                 </td>
1000                 <td>
1001                 <ul>
1002                         <li>GUI bugs resolved</li>
1003                         <li>Runs with -nodisplay from command line</li>
1004                 </ul>
1005                 </td>
1006         </tr>
1007         <tr>
1008                 <td height="63">
1009                 <div align="center"><strong>2.05b</strong><br>
1010                 15/9/05</div>
1011                 </td>
1012                 <td>
1013                 <ul>
1014                         <li>Choose EPS export as lineart or text</li>
1015                         <li>Jar files are executable</li>
1016                         <li>Can read in Uracil - maps to unknown residue</li>
1017                 </ul>
1018                 </td>
1019                 <td>
1020                 <ul>
1021                         <li>Known OutOfMemory errors give warning message</li>
1022                         <li>Overview window calculated more efficiently</li>
1023                         <li>Several GUI bugs resolved</li>
1024                 </ul>
1025                 </td>
1026         </tr>
1027         <tr>
1028                 <td>
1029                 <div align="center"><strong>2.05</strong><br>
1030                 30/8/05</div>
1031                 </td>
1032                 <td>
1033                 <ul>
1034                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
1035                 </ul>
1036                 </td>
1037                 <td>
1038                 <ul>
1039                         <li>Several GUI bugs resolved</li>
1040                 </ul>
1041                 </td>
1042         </tr>
1043         <tr>
1044                 <td>
1045                 <div align="center"><strong>2.04</strong><br>
1046                 24/8/05</div>
1047                 </td>
1048                 <td>
1049                 <ul>
1050                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
1051                 </ul>
1052                 </td>
1053                 <td>
1054                 <ul>
1055                         <li>Improved JPred client reliability</li>
1056                         <li>Improved loading of Jalview files</li>
1057                 </ul>
1058                 </td>
1059         </tr>
1060         <tr>
1061                 <td>
1062                 <div align="center"><strong>2.03</strong><br>
1063                 18/8/05</div>
1064                 </td>
1065                 <td>
1066                 <ul>
1067                         <li>Set Proxy server name and port in preferences</li>
1068                         <li>Multiple URL links from sequence ids</li>
1069                         <li>User Defined Colours can have a scheme name and added to
1070                         Colour Menu</li>
1071                         <li>Choose to ignore gaps in consensus calculation</li>
1072                         <li>Unix users can set default web browser</li>
1073                         <li>Runs without GUI for batch processing</li>
1074                         <li>Dynamically generated Web Service Menus</li>
1075                 </ul>
1076                 </td>
1077                 <td>
1078                 <ul>
1079                         <li>InstallAnywhere download for Sparc Solaris</li>
1080                 </ul>
1081                 </td>
1082         </tr>
1083         <tr>
1084                 <td>
1085                 <div align="center"><strong>2.02</strong><br>
1086                 18/7/05</div>
1087                 </td>
1088                 <td>&nbsp;</td>
1089                 <td>
1090                 <ul>
1091                         <li>Copy &amp; Paste order of sequences maintains alignment
1092                         order.</li>
1093                 </ul>
1094                 </td>
1095         </tr>
1096         <tr>
1097                 <td>
1098                 <div align="center"><strong>2.01</strong><br>
1099                 12/7/05</div>
1100                 </td>
1101                 <td>
1102                 <ul>
1103                         <li>Use delete key for deleting selection.</li>
1104                         <li>Use Mouse wheel to scroll sequences.</li>
1105                         <li>Help file updated to describe how to add alignment
1106                         annotations.</li>
1107                         <li>Version and build date written to build properties file.</li>
1108                         <li>InstallAnywhere installation will check for updates at
1109                         launch of Jalview.</li>
1110                 </ul>
1111                 </td>
1112                 <td>
1113                 <ul>
1114                         <li>Delete gaps bug fixed.</li>
1115                         <li>FileChooser sorts columns.</li>
1116                         <li>Can remove groups one by one.</li>
1117                         <li>Filechooser icons installed.</li>
1118                         <li>Finder ignores return character when searching. Return key
1119                         will initiate a search.<br>
1120                         </li>
1121                 </ul>
1122                 </td>
1123         </tr>
1124         <tr>
1125                 <td>
1126                 <div align="center"><strong>2.0</strong><br>
1127                 20/6/05</div>
1128                 </td>
1129                 <td>
1130                 <ul>
1131                         <li>New codebase</li>
1132                 </ul>
1133                 </td>
1134                 <td>&nbsp;</td>
1135         </tr>
1136 </table>
1137 <p>&nbsp;</p>
1138 </body>
1139 </html>