X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_8_1.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_8_1.md;h=67ea04721a374146708e955c1f7bc1e632da6248;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=0000000000000000000000000000000000000000;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

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+---
+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
+- <!--  possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 --> Null Pointer Exceptions raised when sorting by feature with lots of groups
+- <!-- JAL-1476 Work in progress - don't send junk to Jmol --> 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