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