X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=1fdf0f245de96e7b34b77a1252871d4f37bf7d9a;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=2d51647148790b1f8d7e7f117e3f2caaee111302;hpb=2c0245a6e119e7a995691cbf35944ae5741b181c;p=jalview.git
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Release History
@@ -33,12 +34,229 @@
Issues Resolved
+
+ |
+
+
+ General
+
+ - Internationalisation of user interface (usually called
+ i18n support) and translation for Spanish locale
+ - Define/Undefine group on current selection with
+ Ctrl-G/Shift Ctrl-G
+ - Improved group creation/removal options in
+ alignment/sequence Popup menu
+ - Sensible precision for symbol distribution percentages
+ shown in logo tooltip.
+ - Annotation panel height set according to amount of
+ annotation when alignment first opened
+ Application
+
+ - Interactive consensus RNA secondary structure prediction
+ VIENNA RNAAliFold JABA 2.1 service
+ - Select columns containing particular features from Feature
+ Settings dialog
+ - View all 'representative' PDB structures for selected
+ sequences
+ - Update Jalview project format:
+
+ - New file extension for Jalview projects '.jvp'
+ - Preserve sequence and annotation dataset (to store
+ secondary structure annotation,etc)
+ - Per group and alignment annotation and RNA helix
+ colouring
+
+
+ - New similarity measures for PCA and Tree calculation
+ (PAM250)
+ - Experimental support for retrieval and viewing of flanking
+ regions for an alignment
+
+ |
+
+ Application
+
+ - logo keeps spinning and status remains at queued or
+ running after job is cancelled
+ - cannot export features from alignments imported from
+ Jalview/VAMSAS projects
+ - Buggy slider for web service parameters that take float
+ values
+ - Newly created RNA secondary structure line doesn't have
+ 'display all symbols' flag set
+ - T-COFFEE alignment score shading scheme and other
+ annotation shading not saved in jalview project
+ - Local file cannot be loaded in freshly downloaded Jalview
+ - Jalview icon not shown on dock in Mountain Lion/Webstart
+ - Load file from desktop file browser fails
+ - Occasional NPE thrown when calculating large trees
+ - Cannot reorder or slide sequences after dragging an
+ alignment onto desktop
+ - Colour by annotation dialog throws NPE after using
+ 'extract scores' function
+ - Loading/cut'n'pasting an empty file leads to a grey
+ alignment window
+ - Disorder thresholds rendered incorrectly after performing
+ IUPred disorder prediction
+ - Multiple group annotated consensus rows shown when
+ changing 'normalise logo' display setting
+ - Find shows blank dialog after 'finished searching' if
+ nothing matches query
+ - Null Pointer Exceptions raised when sorting by feature
+ with lots of groups
+
+ - Errors in Jmol console when structures in alignment don't
+ overlap
+
+ - Not all working JABAWS services are shown in Jalview's
+ menu
+ - JAVAWS version of jalview fails to launch with 'invalid
+ literal/length code'
+ - Annotation/RNA Helix colourschemes cannot be applied to
+ alignment with groups (actually fixed in 2.8.0b1)
+ - RNA Helices and T-Coffee Scores available as default colourscheme
+
+ Applet
+
+ - Remove group option is shown even when selection is not a
+ group
+ - Apply to all groups ticked but colourscheme changes don't
+ affect groups
+ - Documented RNA Helices and T-Coffee Scores as valid colourscheme name
+ - Annotation labels drawn on sequence IDs when Annotation panel is not displayed
+ - Increased font size for dropdown menus on OSX and embedded windows
+ Other
+
+ - Consensus sequence for alignments/groups with a single
+ sequence were not calculated
+ - annotation files that contain only groups imported as
+ annotation and junk sequences
+ - Fasta files with sequences containing '*' incorrectly
+ recognised as PFAM or BLC
+ - conservation/PID slider apply all groups option doesn't
+ affect background (2.8.0b1)
+
+ - redundancy highlighting is erratic at 0% and 100%
+ - Remove gapped columns fails for sequences with ragged
+ trailing gaps
+ - AMSA annotation row with leading spaces is not registered
+ correctly on import
+ - Jalview crashes when selecting PCA analysis for certain
+ alignments
+ - Opening the colour by annotation dialog for an existing
+ annotation based 'use original colours' colourscheme loses
+ original colours setting
+
+ |
+
+
+ |
+ |
+
+
+ - Trusted certificates for JalviewLite applet and
+ Jalview Desktop application
Certificate was donated by
+ Certum to the Jalview
+ open source project).
+
+ - Jalview SRS links replaced by Uniprot and EBI-search
+
+ - Output in Stockholm format
+ - Allow import of data from gzipped files
+ - Export/import group and sequence associated line
+ graph thresholds
+ - Nucleotide substitution matrix that supports RNA and
+ ambiguity codes
+ - Allow disorder predictions to be made on the current
+ selection (or visible selection) in the same way that JPred
+ works
+ - Groovy scripting for headless jalview operation
+ Other improvements
+
+ - Upgrade desktop installer to InstallAnywhere 2013
+ - COMBINE statement uses current SEQUENCE_REF and
+ GROUP_REF scope to group annotation rows
+ - Support '' style escaping of quotes in Newick
+ files
+ - Group options for JABAWS service by command line name
+ - Empty tooltip shown for JABA service options with a
+ link but no description
+ - Select primary source when selecting authority in
+ database fetcher GUI
+ - Add .mfa to FASTA file extensions recognised by
+ Jalview
+ - Annotation label tooltip text wrap
+
+ |
+
+
+ - Slow scrolling when lots of annotation rows are
+ displayed
+ - Lots of NPE (and slowness) after creating RNA
+ secondary structure annotation line
+ - Sequence database accessions not imported when
+ fetching alignments from Rfam
+ - Incorrect SHMR submission for sequences with
+ identical IDs
+ - View all structures does not always superpose
+ structures
+ - Option widgets in service parameters not updated to
+ reflect user or preset settings
+ - Null pointer exceptions for some services without
+ presets or adjustable parameters
+ - Discover PDB IDs entry in structure menu doesn't
+ discover PDB xRefs
+ - Exception encountered while trying to retrieve
+ features with DAS
+ - Lowest value in annotation row isn't coloured
+ when colour by annotation (per sequence) is coloured
+ - Keyboard mode P jumps to start of gapped region when
+ residue follows a gap
+ - Jalview appears to hang importing an alignment with
+ Wrap as default or after enabling Wrap
+ - 'Right click to add annotations' message
+ shown in wrap mode when no annotations present
+ - Disorder predictions fail with NPE if no automatic
+ annotation already exists on alignment
+ - oninit javascript function should be called after
+ initialisation completes
+ - Remove redundancy after disorder prediction corrupts
+ alignment window display
+ - Example annotation file in documentation is invalid
+ - Grouped line graph annotation rows are not exported
+ to annotation file
+ - Multi-harmony analysis cannot be run when only two
+ groups created
+ - Cannot create multiple groups of line graphs with
+ several 'combine' statements in annotation file
+ - Pressing return several times causes Number Format
+ exceptions in keyboard mode
+ - Multi-harmony (SHMMR) method doesn't submit
+ correct partitions for input data
+ - Translation from DNA to Amino Acids fails
+ - Jalview fail to load newick tree with quoted label
+ - --headless flag isn't understood
+ - ClassCastException when generating EPS in headless
+ mode
+ - Adjusting sequence-associated shading threshold only
+ changes one row's threshold
+ - Preferences and Feature settings panel panel
+ doesn't open
+ - hide consensus histogram also hides conservation and
+ quality histograms
+
+ |
+
|
Application
- Support for JABAWS 2.0 Services (AACon alignment
+ - Support for JABAWS 2.0 Services (AACon alignment
conservation, protein disorder and Clustal Omega)
- JABAWS server status indicator in Web Services preferences
|