+
|
- 2.4
- Feb/2008
+ 2.4.1
+ Not Yet Released
|
- - New VAMSAS capabilities in Jalview
+
- Enable or disable non-positional feature and database references in sequence ID tooltip from View menu in application.
+
+ - URL links generated from description line for regular-expression based URL links (applet and application)
+
+ - Non-positional features displayed in sequence ID tooltip on applet
+
+ - Non-positional feature URL links are shown in link menu (applet and application)
+
+
+ |
+
+
+ - URL links generated for all feature links (bugfix)
+ - Dasobert generated non-positional feature URL link text excludes the start_end suffix (application)
+ - Added URL embedding instructions to features file documentation.
+
+ |
+
+
+
+ |
+ 2.4
+ 27/8//2008
+ |
+
+ User Interface
- - treenode binding for VAMSAS tree exchange
- - local editing and update of sequences in VAMSAS alignments
- (experimental)
- - Create new or select existing session to join
- - load and save of vamsas documents
-
-
- Retrieval of cross-referenced sequences from other databases
-
- export annotation rows as CSV for spreadsheet import
- Jalview projects record alignment dataset associations, EMBL
- products, and cDNA sequence mappings
Linked highlighting of codon and amino acid from translation
and protein products
+ Linked highlighting of structure associated with residue mapping to codon position
+ Sequence Fetcher provides example accession numbers and 'clear' button
+ MemoryMonitor added as an option under Desktop's Tools menu
+ Extract score function to parse whitespace separated numeric data in description line
+ Column labels in alignment annotation can be centred.
+ Tooltip for sequence associated annotation give name of sequence
+
+ Web Services and URL fetching
+
- JPred3 web service
+ - Prototype sequence search client (no public services available yet)
+ - Fetch either seed alignment or full alignment from PFAM
+ - URL Links created for matching database cross references as well as sequence ID
+ - URL Links can be created using regular-expressions
+
+ Sequence Database Connectivity
+
+ - Retrieval of cross-referenced sequences from other databases
+
- Generalised database reference retrieval and validation to
all fetchable databases
- Fetch sequences from DAS sources supporting the sequence command
- - Sequence Fetcher GUI provides example accession numbers and 'clear' button
- - Application command line
+
+ Import and Export
+ export annotation rows as CSV for spreadsheet import
+ Jalview projects record alignment dataset associations, EMBL
+ products, and cDNA sequence mappings
+ Sequence Group colour can be specified in Annotation File
+ Ad-hoc colouring of group in Annotation File using RGB triplet as name of colourscheme
+
+ VAMSAS Client capabilities (Experimental)
+
+ - treenode binding for VAMSAS tree exchange
+ - local editing and update of sequences in VAMSAS alignments
+ (experimental)
+ - Create new or select existing session to join
+ - load and save of vamsas documents
+
+ Application command line
- -tree parameter to open trees (introduced for passing from
applet)
@@ -55,32 +102,27 @@
- -groovy command line argument executes a given groovy
script after all input data has been loaded and parsed
-
- Trees passed as applet parameters can be passed to
+ Applet-Application data exchange
+
+ - Trees passed as applet parameters can be passed to
application (when using "View in full application")
- - MemoryMonitor added as an option under Desktop's Tools menu
-
- - allow reading of JPred concise files as a normal filetype
- - sort sequences by named annotation scores
- - Re-instated Full AMSA support and .amsa file association
- - Stockholm annotation parsing and alignment properties import
-
- - Applet Parameters
+
+ Applet Parameters
- feature group display control parameter
- debug parameter
+ - showbutton parameter
-
- Applet API methods
+ Applet API methods
- newView public method
- Window (current view) specific get/set public methods
- Feature display control methods
+ - get list of currently selected sequences
-
-
- New Jalview distribution features
+ New Jalview distribution features
+ - InstallAnywhere Installer upgraded to IA 2008 VP1
- RELEASE file gives build properties for the latest Jalview
release.
- Java 1.1 Applet build made easier and donotobfuscate
@@ -89,9 +131,9 @@
- Debug flag for javacc
- .jalview_properties file is documented (slightly) in
jalview.bin.Cache
- - Group colour can be given as an RGB triplet which is used to colour all non-gap characters
-
+ - Continuous Build Integration for stable and development version of Application, Applet and source distribution
+
|
@@ -116,6 +158,7 @@
- better reporting of non-fatal warnings to user when file
parsing fails.
- Save works when Jalview project is default format
+ - Save as dialog opened if current alignment format is not a valid output format
- Uniprot canonical names introduced for both das and vamsas
- Histidine should be midblue (not pink!) in Zappo
- error messages passed up and output when data read fails
@@ -123,6 +166,10 @@
is edited
- allow PDB files without pdb ID HEADER lines (like those
generated by MODELLER) to be read in properly
+ - allow reading of JPred concise files as a normal filetype
+ - Stockholm annotation parsing and alignment properties import fixed for PFAM records
+
+ - Structure view windows have correct name in Desktop window list
- annotation consisting of sequence associated scores can be
read and written correctly to annotation file
- Aligned cDNA translation to aligned peptide works correctly
@@ -136,8 +183,19 @@
- Secondary structure lines are drawn starting from first
column of alignment
- Uniprot XML import updated for new schema release in July 2008
+ - Sequence feature to sequence ID match for Features file is case-insensitive
+ - Sequence features read from Features file appended to all sequences with matching IDs
+ - PDB structure coloured correctly for associated views containing a sub-sequence
+ - PDB files can be retrieved by applet from Jar files
+ - feature and annotation file applet parameters referring to different directories are retrieved correctly
-
+ - Fixed application hang whilst waiting for splash-screen version check to complete
+ - Applet properly URLencodes input parameter values when passing them to the launchApp service
+ - display name and local features preserved in results retrieved from web service
+ - Visual delay indication for sequence retrieval and sequence fetcher initialisation
+ - updated Application to use DAS 1.53e version of dasobert DAS client
+ - Re-instated Full AMSA support and .amsa file association
+ - Fixed parsing of JNet Concise annotation sans sequences
|