order by feature documentation
[jalview.git] / help / html / releases.html
1 <html>
2 <head>
3 <title>Release History</title>
4 </head>
5 <body>
6 <p><strong>Release History</strong></p>
7 <table border="1">
8         <tr>
9                 <td width="60" nowrap>
10                 <div align="center"><em><strong>Release</strong></em></div>
11                 </td>
12                 <td>
13                 <div align="center"><em><strong>New Features</strong></em></div>
14                 </td>
15                 <td>
16                 <div align="center"><em><strong>Issues Resolved</strong></em></div>
17                 </td>
18         </tr>
19         <tr>
20         
21                 <td>
22                 <div align="center"><strong>2.4.1</strong><br>
23                 <em>Not Yet Released</em></div>
24                 </td>
25                 <td>
26                 <ul>
27                 <li>Fetch DB References capabilities and UI expanded to support retrieval from DAS sequence sources</li> 
28                 <li>Local DAS Sequence sources can be added via the command line or via the Add local source dialog box.</li>
29                 <li>Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
30                 </li>
31                 <li>URL links generated from description line for regular-expression based URL links (applet and application)
32                 </li>
33                 <li>Non-positional features displayed in sequence ID tooltip on applet
34                 </li>
35                 <li>Non-positional feature URL links are shown in link menu (applet and application)
36                 </li>
37                 <li>Automatic Scrolling option in View menu to display the currently highlighted region of an alignment.
38                 </li>
39                 <li>Improved VAMSAS synchronization (jalview archive used to preserve views, structures, and tree display settings)
40                 </li>
41                 <li>Sharing of selected regions between views and with other VAMSAS applications (Experimental feature!)
42                 </li>
43                 <li>New hidden columns and rows and representatives capabilities in annotations file (in progress - not yet fully implemented)</li>
44                 <li>Order an alignment in order of average feature score or total feature count</li> 
45                 </ul>
46                 </td>
47                 <td>
48                 <ul>
49                 <li>Better handling of exceptions during sequence retrieval</li>
50                 <li>URL links generated for all feature links (bugfix)</li>
51                 <li>Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)</li>
52                 <li>Added URL embedding instructions to features file documentation.</li>
53                 <li>Sequences are now validated against EMBL database (broken in Version 2.4.0)</li>
54                 <li>Codons containing ambiguous nucleotides translated as 'X' in peptide product</li>
55                 <li>Sequence description lines properly shared via VAMSAS</li>
56                 <li>Match case switch in find dialog box works for both sequence ID and sequence string and query strings do not have to be in upper case to match case-insensitively.</li>
57                 </ul>
58                 </td>
59         
60         </tr>
61         <tr>
62                 <td>
63                 <div align="center"><strong>2.4</strong><br>
64                 27/8//2008</div>
65                 </td>
66                 <td>
67                         <em>User Interface</em>
68                         <ul>
69                         <li>Linked highlighting of codon and amino acid from translation
70                         and protein products</li>
71                         <li>Linked highlighting of structure associated with residue mapping to codon position</li>
72                         <li>Sequence Fetcher provides example accession numbers and 'clear' button</li>
73                         <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
74                         <li>Extract score function to parse whitespace separated numeric data in description line</li>
75                         <li>Column labels in alignment annotation can be centred.</li>
76                         <li>Tooltip for sequence associated annotation give name of sequence</li>
77                         </ul>
78                         <em>Web Services and URL fetching</em>
79                         <ul>
80                         <li>JPred3 web service</li>
81                         <li>Prototype sequence search client (no public services available yet)</li>
82                         <li>Fetch either seed alignment or full alignment from PFAM</li>
83                         <li>URL Links created for matching database cross references as well as sequence ID</li> 
84                         <li>URL Links can be created using regular-expressions</li>
85                         </ul>
86                 <em>Sequence Database Connectivity</em>
87                         <ul>
88                         <li>Retrieval of cross-referenced sequences from other databases
89                         </li>
90                         <li>Generalised database reference retrieval and validation to
91                         all fetchable databases</li>
92                         <li>Fetch sequences from DAS sources supporting the sequence command</li>
93                         </ul>
94                         <em>Import and Export</em>
95                         <li>export annotation rows as CSV for spreadsheet import</li>
96                         <li>Jalview projects record alignment dataset associations, EMBL
97                         products, and cDNA sequence mappings</li>
98                         <li>Sequence Group colour can be specified in Annotation File</li>
99                         <li>Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme</li>
100                         </ul>
101                 <em>VAMSAS Client capabilities (Experimental)</em>
102                         <ul>
103                                 <li>treenode binding for VAMSAS tree exchange</li>
104                                 <li>local editing and update of sequences in VAMSAS alignments
105                                 (experimental)</li>
106                                 <li>Create new or select existing session to join</li>
107                                 <li>load and save of vamsas documents</li>
108                         </ul>
109         <em>Application command line</em>
110                         <ul>
111                                 <li>-tree parameter to open trees (introduced for passing from
112                                 applet)</li>
113                                 <li>-fetchfrom command line argument to specify nicknames of
114                                 DAS servers to query for alignment features</li>
115                                 <li>-dasserver command line argument to add new servers that
116                                 are also automatically queried for features</li>
117                                 <li>-groovy command line argument executes a given groovy
118                                 script after all input data has been loaded and parsed</li>
119                         </ul>
120         <em>Applet-Application data exchange</em>       
121                 <ul>
122                 <li>Trees passed as applet parameters can be passed to
123                         application (when using &quot;View in full application&quot;)</li>
124                 </ul>
125         <em>Applet Parameters</em>
126                         <ul>
127                                 <li>feature group display control parameter</li>
128                                 <li>debug parameter</li>
129                                 <li>showbutton parameter</li>
130                         </ul>
131         <em>Applet API methods</em>
132                         <ul>
133                                 <li>newView public method</li>
134                                 <li>Window (current view) specific get/set public methods</li>
135                                 <li>Feature display control methods</li>
136                                 <li>get list of currently selected sequences</li>
137                         </ul>
138         <em>New Jalview distribution features</em>
139                 <ul>
140                         <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li> 
141                         <li>RELEASE file gives build properties for the latest Jalview
142                         release.</li>
143                         <li>Java 1.1 Applet build made easier and donotobfuscate
144                         property controls execution of obfuscator</li>
145                         <li>Build target for generating source distribution</li>
146                         <li>Debug flag for javacc</li>
147                         <li>.jalview_properties file is documented (slightly) in
148                         jalview.bin.Cache</li>
149             <li>Continuous Build Integration for stable and development version of Application, Applet and source distribution</li>             
150                 </ul>
151                 
152                 </td>
153                 <td>
154                 <ul>
155                         <li>selected region output includes visible annotations (for
156                         certain formats)</li>
157                         <li>edit label/displaychar contains existing label/char for
158                         editing</li>
159                         <li>update PDBEntries when DBRefEntries change (vamsas)</li>
160                         <li>shorter peptide product names from EMBL records</li>
161                         <li>Newick string generator makes compact representations</li>
162                         <li>bootstrap values parsed correctly for tree files with
163                         comments</li>
164                         <li>pathological filechooser bug avoided by not allowing
165                         filenames containing a ':'</li>
166                         <li>Fixed exception when parsing GFF files containing global
167                         sequence features</li>
168                         <li>Alignment datasets are finalized only when number of
169                         references from alignment sequences goes to zero</li>
170                         <li>Close of tree branch colour box without colour selection
171                         causes cascading exceptions</li>
172                         <li>occasional negative imgwidth exceptions</li>
173                         <li>better reporting of non-fatal warnings to user when file
174                         parsing fails.</li>
175                         <li>Save works when Jalview project is default format</li>
176                         <li>Save as dialog opened if current alignment format is not a valid output format</li>
177                         <li>Uniprot canonical names introduced for both das and vamsas</li>
178                         <li>Histidine should be midblue (not pink!) in Zappo</li>
179                         <li>error messages passed up and output when data read fails</li>
180                         <li>edit undo recovers previous dataset sequence when sequence
181                         is edited</li>
182                         <li>allow PDB files without pdb ID HEADER lines (like those
183                         generated by MODELLER) to be read in properly</li>
184                         <li>allow reading of JPred concise files as a normal filetype</li>
185                         <li>Stockholm annotation parsing and alignment properties import fixed for PFAM records
186                         </li>
187                         <li>Structure view windows have correct name in Desktop window list</li>
188                         <li>annotation consisting of sequence associated scores can be
189                         read and written correctly to annotation file</li>
190                         <li>Aligned cDNA translation to aligned peptide works correctly
191                         </li>
192                         <li>Fixed display of hidden sequence markers and non-italic font
193                         for representatives in Applet</li>
194                         <li>Applet Menus are always embedded in applet window on Macs.</li>
195                         <li>Newly shown features appear at top of stack (in Applet)</li>
196                         <li>Annotations added via parameter not drawn properly due to
197                         null pointer exceptions</li>
198                         <li>Secondary structure lines are drawn starting from first
199                         column of alignment</li>
200                         <li>Uniprot XML import updated for new schema release in July 2008</li>
201                         <li>Sequence feature to sequence ID match for Features file is case-insensitive</li>
202                         <li>Sequence features read from Features file appended to all sequences with matching IDs</li>
203                         <li>PDB structure coloured correctly for associated views containing a sub-sequence</li>
204                         <li>PDB files can be retrieved by applet from Jar files</li>
205                         <li>feature and annotation file applet parameters referring to different directories are retrieved correctly</li>   
206                         <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
207                         <li>Fixed application hang whilst waiting for splash-screen version check to complete</li>
208                         <li>Applet properly URLencodes input parameter values when passing them to the launchApp service</li>
209                         <li>display name and local features preserved in results retrieved from web service</li> 
210                         <li>Visual delay indication for sequence retrieval and sequence fetcher initialisation</li>
211                         <li>updated Application to use DAS 1.53e version of dasobert DAS client</li>
212                         <li>Re-instated Full AMSA support and .amsa file association</li>
213                         <li>Fixed parsing of JNet Concise annotation <em>sans</em> sequences</li>  
214                 </ul>
215                 </td>
216         </tr>
217         <tr>
218         <td>
219                 <div align="center"><strong>2.3</strong><br>
220                 9/5/07</div>
221                 </td>
222                 <td>
223                 <ul>
224                         <li>Jmol 11.0.2 integration</li>
225                         <li>PDB views stored in Jalview XML files</li>
226                         <li>Slide sequences</li>
227                         <li>Edit sequence in place</li>
228                         <li>EMBL CDS features</li>
229                         <li>DAS Feature mapping</li>
230                         <li>Feature ordering</li>
231                         <li>Alignment Properties</li>
232                         <li>Annotation Scores</li>
233                         <li>Sort by scores</li>
234                         <li>Feature/annotation editing in applet</li>
235                 </ul>
236                 </td>
237                 <td>
238                 <ul>
239                         <li>Headless state operation in 2.2.1</li>
240                         <li>Incorrect and unstable DNA pairwise alignment</li>
241                         <li>Cut and paste of sequences with annotation</li>
242                         <li>Feature group display state in XML</li>
243                         <li>Feature ordering in XML</li>
244                         <li>blc file iteration selection using filename # suffix</li>
245                         <li>Stockholm alignment properties</li>
246                         <li>Stockhom alignment secondary structure annotation</li>
247                         <li>2.2.1 applet had no feature transparency</li>
248                         <li>Number pad keys can be used in cursor mode</li>
249                         <li>Structure Viewer mirror image resolved</li>
250                 </ul>
251                 </td>
252
253         </tr>
254         <tr>
255                 <td>
256                 <div align="center"><strong>2.2.1</strong><br>
257                 12/2/07</div>
258                 </td>
259                 <td>
260                 <ul>
261                         <li>Non standard characters can be read and displayed
262                         <li>Annotations/Features can be imported/exported to the applet
263                         via textbox
264                         <li>Applet allows editing of sequence/annotation/group name
265                         &amp; description
266                         <li>Preference setting to display sequence name in italics
267                         <li>Annotation file format extended to allow Sequence_groups to
268                         be defined
269                         <li>Default opening of alignment overview panel can be specified
270                         in preferences
271                         <li>PDB residue numbering annotation added to associated
272                         sequences
273                 </ul>
274                 </td>
275                 <td>
276                 <ul>
277                         <li>Applet crash under certain Linux OS with Java 1.6 installed
278                         <li>Annotation file export / import bugs fixed
279                         <li>PNG / EPS image output bugs fixed
280                 </ul>
281                 </td>
282         </tr>
283         <tr>
284                 <td>
285                 <div align="center"><strong>2.2</strong><br>
286                 27/11/06</div>
287                 </td>
288                 <td>
289                 <ul>
290                         <li>Multiple views on alignment
291                         <li>Sequence feature editing
292                         <li>&quot;Reload&quot; alignment
293                         <li>&quot;Save&quot; to current filename
294                         <li>Background dependent text colour
295                         <li>Right align sequence ids
296                         <li>User-defined lower case residue colours
297                         <li>Format Menu
298                         <li>Select Menu
299                         <li>Menu item accelerator keys
300                         <li>Control-V pastes to current alignment
301                         <li>Cancel button for DAS Feature Fetching
302                         <li>PCA and PDB Viewers zoom via mouse roller
303                         <li>User-defined sub-tree colours and sub-tree selection
304                         <li>'New Window' button on the 'Output to Text box'
305                 </ul>
306                 </td>
307                 <td>
308                 <ul>
309                         <li>New memory efficient Undo/Redo System
310                         <li>Optimised symbol lookups and conservation/consensus
311                         calculations
312                         <li>Region Conservation/Consensus recalculated after edits
313                         <li>Fixed Remove Empty Columns Bug (empty columns at end of
314                         alignment)
315                         <li>Slowed DAS Feature Fetching for increased robustness.
316                         <li>Made angle brackets in ASCII feature descriptions display
317                         correctly
318                         <li>Re-instated Zoom function for PCA
319                         <li>Sequence descriptions conserved in web service analysis
320                         results
321                         <li>Uniprot ID discoverer uses any word separated by &#8739;
322                         <li>WsDbFetch query/result association resolved
323                         <li>Tree leaf to sequence mapping improved
324                         <li>Smooth fonts switch moved to FontChooser dialog box.
325                 </ul>
326                 </td>
327         </tr>
328         <tr>
329                 <td>
330                 <div align="center"><strong>2.1.1</strong><br>
331                 12/9/06</div>
332                 </td>
333                 <td>
334                 <ul>
335                         <li>Copy consensus sequence to clipboard</li>
336                 </ul>
337                 </td>
338                 <td>
339                 <ul>
340                         <li>Image output - rightmost residues are rendered if sequence
341                         id panel has been resized</li>
342                         <li>Image output - all offscreen group boundaries are rendered</li>
343                         <li>Annotation files with sequence references - all elements in
344                         file are relative to sequence position</li>
345                         <li>Mac Applet users can use Alt key for group editing</li>
346                 </ul>
347                 </td>
348         </tr>
349         <tr>
350                 <td>
351                 <div align="center"><strong>2.1</strong><br>
352                 22/8/06</div>
353                 </td>
354                 <td>
355                 <ul>
356                         <li>MAFFT Multiple Alignment in default Web Service list</li>
357                         <li>DAS Feature fetching</li>
358                         <li>Hide sequences and columns</li>
359                         <li>Export Annotations and Features</li>
360                         <li>GFF file reading / writing</li>
361                         <li>Associate structures with sequences from local PDB files</li>
362                         <li>Add sequences to exisiting alignment</li>
363                         <li>Recently opened files / URL lists</li>
364                         <li>Applet can launch the full application</li>
365                         <li>Applet has transparency for features (Java 1.2 required)</li>
366                         <li>Applet has user defined colours parameter</li>
367                         <li>Applet can load sequences from parameter &quot;sequence<em>x</em>&quot;</li>
368                 </ul>
369                 </td>
370                 <td>
371                 <ul>
372                         <li>Redundancy Panel reinstalled in the Applet</li>
373                         <li>Monospaced font - EPS / rescaling bug fixed</li>
374                         <li>Annotation files with sequence references bug fixed</li>
375                 </ul>
376                 </td>
377         </tr>
378         <tr>
379                 <td>
380                 <div align="center"><strong>2.08.1</strong><br>
381                 2/5/06</div>
382                 </td>
383                 <td>
384                 <ul>
385                         <li>Change case of selected region from Popup menu</li>
386                         <li>Choose to match case when searching</li>
387                         <li>Middle mouse button and mouse movement can compress / expand
388                         the visible width and height of the alignment</li>
389                 </ul>
390                 </td>
391                 <td>
392                 <ul>
393                         <li>Annotation Panel displays complete JNet results</li>
394                 </ul>
395                 </td>
396         </tr>
397         <tr>
398                 <td>
399                 <div align="center"><strong>2.08b</strong><br>
400                 18/4/06</div>
401                 </td>
402                 <td>&nbsp;</td>
403                 <td>
404                 <ul>
405                         <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
406                         <li>Righthand label on wrapped alignments shows correct value</li>
407                 </ul>
408                 </td>
409         </tr>
410         <tr>
411                 <td>
412                 <div align="center"><strong>2.08</strong><br>
413                 10/4/06</div>
414                 </td>
415                 <td>
416                 <ul>
417                         <li>Editing can be locked to the selection area</li>
418                         <li>Keyboard editing</li>
419                         <li>Create sequence features from searches</li>
420                         <li>Precalculated annotations can be loaded onto alignments</li>
421                         <li>Features file allows grouping of features</li>
422                         <li>Annotation Colouring scheme added</li>
423                         <li>Smooth fonts off by default - Faster rendering</li>
424                         <li>Choose to toggle Autocalculate Consensus On/Off</li>
425                 </ul>
426                 </td>
427                 <td>
428                 <ul>
429                         <li>Drag &amp; Drop fixed on Linux</li>
430                         <li>Jalview Archive file faster to load/save, sequence
431                         descriptions saved.</li>
432                 </ul>
433                 </td>
434         </tr>
435         <tr>
436                 <td>
437                 <div align="center"><strong>2.07</strong><br>
438                 12/12/05</div>
439                 </td>
440                 <td>
441                 <ul>
442                         <li>PDB Structure Viewer enhanced</li>
443                         <li>Sequence Feature retrieval and display enhanced</li>
444                         <li>Choose to output sequence start-end after sequence name for
445                         file output</li>
446                         <li>Sequence Fetcher WSDBFetch@EBI</li>
447                         <li>Applet can read feature files, PDB files and can be used for
448                         HTML form input</li>
449                 </ul>
450                 </td>
451                 <td>
452                 <ul>
453                         <li>HTML output writes groups and features</li>
454                         <li>Group editing is Control and mouse click</li>
455                         <li>File IO bugs</li>
456                 </ul>
457                 </td>
458         </tr>
459         <tr>
460                 <td>
461                 <div align="center"><strong>2.06</strong><br>
462                 28/9/05</div>
463                 </td>
464                 <td>
465                 <ul>
466                         <li>View annotations in wrapped mode</li>
467                         <li>More options for PCA viewer</li>
468                 </ul>
469                 </td>
470                 <td>
471                 <ul>
472                         <li>GUI bugs resolved</li>
473                         <li>Runs with -nodisplay from command line</li>
474                 </ul>
475                 </td>
476         </tr>
477         <tr>
478                 <td height="63">
479                 <div align="center"><strong>2.05b</strong><br>
480                 15/9/05</div>
481                 </td>
482                 <td>
483                 <ul>
484                         <li>Choose EPS export as lineart or text</li>
485                         <li>Jar files are executable</li>
486                         <li>Can read in Uracil - maps to unknown residue</li>
487                 </ul>
488                 </td>
489                 <td>
490                 <ul>
491                         <li>Known OutOfMemory errors give warning message</li>
492                         <li>Overview window calculated more efficiently</li>
493                         <li>Several GUI bugs resolved</li>
494                 </ul>
495                 </td>
496         </tr>
497         <tr>
498                 <td>
499                 <div align="center"><strong>2.05</strong><br>
500                 30/8/05</div>
501                 </td>
502                 <td>
503                 <ul>
504                         <li>Edit and annotate in &quot;Wrapped&quot; view</li>
505                 </ul>
506                 </td>
507                 <td>
508                 <ul>
509                         <li>Several GUI bugs resolved</li>
510                 </ul>
511                 </td>
512         </tr>
513         <tr>
514                 <td>
515                 <div align="center"><strong>2.04</strong><br>
516                 24/8/05</div>
517                 </td>
518                 <td>
519                 <ul>
520                         <li>Hold down mouse wheel &amp; scroll to change font size</li>
521                 </ul>
522                 </td>
523                 <td>
524                 <ul>
525                         <li>Improved JPred client reliability</li>
526                         <li>Improved loading of Jalview files</li>
527                 </ul>
528                 </td>
529         </tr>
530         <tr>
531                 <td>
532                 <div align="center"><strong>2.03</strong><br>
533                 18/8/05</div>
534                 </td>
535                 <td>
536                 <ul>
537                         <li>Set Proxy server name and port in preferences</li>
538                         <li>Multiple URL links from sequence ids</li>
539                         <li>User Defined Colours can have a scheme name and added to
540                         Colour Menu</li>
541                         <li>Choose to ignore gaps in consensus calculation</li>
542                         <li>Unix users can set default web browser</li>
543                         <li>Runs without GUI for batch processing</li>
544                         <li>Dynamically generated Web Service Menus</li>
545                 </ul>
546                 </td>
547                 <td>
548                 <ul>
549                         <li>InstallAnywhere download for Sparc Solaris</li>
550                 </ul>
551                 </td>
552         </tr>
553         <tr>
554                 <td>
555                 <div align="center"><strong>2.02</strong><br>
556                 18/7/05</div>
557                 </td>
558                 <td>&nbsp;</td>
559                 <td>
560                 <ul>
561                         <li>Copy &amp; Paste order of sequences maintains alignment
562                         order.</li>
563                 </ul>
564                 </td>
565         </tr>
566         <tr>
567                 <td>
568                 <div align="center"><strong>2.01</strong><br>
569                 12/7/05</div>
570                 </td>
571                 <td>
572                 <ul>
573                         <li>Use delete key for deleting selection.</li>
574                         <li>Use Mouse wheel to scroll sequences.</li>
575                         <li>Help file updated to describe how to add alignment
576                         annotations.</li>
577                         <li>Version and build date written to build properties file.</li>
578                         <li>InstallAnywhere installation will check for updates at
579                         launch of Jalview.</li>
580                 </ul>
581                 </td>
582                 <td>
583                 <ul>
584                         <li>Delete gaps bug fixed.</li>
585                         <li>FileChooser sorts columns.</li>
586                         <li>Can remove groups one by one.</li>
587                         <li>Filechooser icons installed.</li>
588                         <li>Finder ignores return character when searching. Return key
589                         will initiate a search.<br>
590                         </li>
591                 </ul>
592                 </td>
593         </tr>
594         <tr>
595                 <td>
596                 <div align="center"><strong>2.0</strong><br>
597                 20/6/05</div>
598                 </td>
599                 <td>
600                 <ul>
601                         <li>New codebase</li>
602                 </ul>
603                 </td>
604                 <td>&nbsp;</td>
605         </tr>
606 </table>
607 <p>&nbsp;</p>
608 </body>
609 </html>