--- channel: release version: 2.8.1 date: 2014-06-04 --- ## New Features ### 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 ## Issues Resolved ### 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