--- /dev/null
+---
+channel: release
+version: 2.7
+date: 2011-09-27
+---
+
+## New Features
+
+
+
+### Application
+- Jalview Desktop News Reader
+- Tweaked default layout of web services menu
+- View/alignment association menu to enable user to easily specify which alignment a multi-structure view takes its colours/correspondences from
+- Allow properties file location to be specified as URL
+- Extend Jalview project to preserve associations between many alignment views and a single Jmol display
+- Store annotation row height in Jalview project file
+- Annotation row column label formatting attributes stored in project file
+- Annotation row order for auto-calculated annotation rows preserved in Jalview project file
+- Visual progress indication when Jalview state is saved using Desktop window menu
+- Visual indication that command line arguments are still being processed
+- Groovy script execution from URL
+- Colour by annotation default min and max colours in preferences
+- Automatically associate PDB files dragged onto an alignment with sequences that have high similarity and matching IDs
+- Update JGoogleAnalytics to latest release (0.3)
+- 'view structures' option to open many structures in same window
+- Sort associated views menu option for tree panel
+- Group all JABA and non-JABA services for a particular analysis function in its own submenu
+
+
+### Applet
+- Userdefined and autogenerated annotation rows for groups
+- Adjustment of alignment annotation pane height
+- Annotation scrollbar for annotation panel
+- Drag to reorder annotation rows in annotation panel
+- 'automaticScrolling' parameter
+- Allow sequences with partial ID string matches to be annotated from GFF/Jalview features files
+- Sequence logo annotation row in applet
+- Absolute paths relative to host server in applet parameters are treated as such
+- New in the JalviewLite javascript API:
+ - JalviewLite.js javascript library
+ - Javascript callbacks for
+ - Applet initialisation
+ - Sequence/alignment mouse-overs and selections
+ - scrollTo row and column alignment scrolling functions
+ - Select sequence/alignment regions from javascript
+ - javascript structure viewer harness to pass messages between Jmol and Jalview when running as distinct applets
+ - sortBy method
+ - Set of applet and application examples shipped with documentation
+ - New example to demonstrate JalviewLite and Jmol javascript message exchange
+
+
+### General
+- Enable Jmol displays to be associated with multiple multiple alignments
+- Option to automatically sort alignment with new tree
+- User configurable link to enable redirects to a www.Jalview.org mirror
+- Jmol colours option for Jmol displays
+- Configurable newline string when writing alignment and other flat files
+- Allow alignment annotation description lines to contain html tags
+
+
+### Documentation and Development
+- Add groovy test harness for bulk load testing to examples
+- Groovy script to load and align a set of sequences using a web service before displaying the result in the Jalview desktop
+- Restructured javascript and applet api documentation
+- Ant target to publish example html files with applet archive
+- Netbeans project for building Jalview from source
+- ant task to create online javadoc for Jalview source
+
+
+## Issues Resolved
+
+
+
+### Application
+- User defined colourscheme throws exception when current built in colourscheme is saved as new scheme
+- AlignFrame->Save in application pops up save dialog for valid filename/format
+- Cannot view associated structure for UniProt sequence
+- PDB file association breaks for UniProt sequence P37173
+- Associate PDB from file dialog does not tell you which sequence is to be associated with the file
+- Find All raises null pointer exception when query only matches sequence IDs
+- Pre 2.6 Jalview project cannot be loaded into v2.6
+- Jalview project with Jmol views created with Jalview 2.4 cannot be loaded
+- Filetype associations not installed for webstart launch
+- Two or more chains in a single PDB file associated with sequences in different alignments do not get coloured by their associated sequence
+- Visibility status of autocalculated annotation row not preserved when project is loaded
+- Annotation row height and visibility attributes not stored in Jalview project
+- Tree bootstraps are not preserved when saved as a Jalview project
+- Envision2 workflow tooltips are corrupted
+- Enabling show group conservation also enables colour by conservation
+- Duplicate group associated conservation or consensus created on new view
+- Annotation scrollbar not displayed after 'show all hidden annotation rows' option selected
+- Alignment quality not updated after alignment annotation row is hidden then shown
+- Preserve colouring of structures coloured by sequences in pre Jalview 2.7 projects
+- Web service job parameter dialog is not laid out properly
+- Web services menu not refreshed after 'reset services' button is pressed in preferences
+- Annotation off by one in Jalview v2_3 example project
+- Structures imported from file and saved in project get name like jalview_pdb1234.txt when reloaded
+- Jalview does not always retrieve progress of a JABAWS job execution in full once it is complete
+
+
+### Applet
+- Alignment height set incorrectly when lots of annotation rows are displayed
+- Relative URLs in feature HTML text not resolved to codebase
+- View follows highlighting does not work for positions in sequences
+- <= shown as = in tooltip
+- Export features raises exception when no features exist
+- Separator string used for serialising lists of IDs for javascript api is modified when separator string provided as parameter
+- Null pointer exception when selecting tree leaves for alignment with no existing selection
+- Relative URLs for datasources assumed to be relative to applet's codebase
+- Status bar not updated after finished searching and search wraps around to first result
+- StructureSelectionManager instance shared between several Jalview applets causes race conditions and memory leaks
+- Hover tooltip and mouseover of position on structure not sent from Jmol in applet
+- Certain sequences of javascript method calls to applet API fatally hang browser
+
+
+### General
+- View follows structure mouseover scrolls beyond position with wrapped view and hidden regions
+- Find sequence position moves to wrong residue with/without hidden columns
+- Sequence length given in alignment properties window is off by 1
+- InvalidNumberFormat exceptions thrown when trying to import PDB like structure files
+- Positional search results are only highlighted between user-supplied sequence start/end bounds
+- End attribute of sequence is not validated
+- Find dialog only finds first sequence containing a given sequence position
+- Sequence numbering not preserved in MSF alignment output
+- Jalview PDB file reader does not extract sequence from nucleotide chains correctly
+- Structure colours not updated when tree partition changed in alignment
+- Sequence associated secondary structure not correctly parsed in interleaved stockholm
+- Colour by annotation dialog does not restore current state
+- Hiding (nearly) all sequences doesn't work properly
+- Sequences containing lowercase letters are not properly associated with their pdb files
+
+
+### Documentation and Development
+- schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright tool
git://source.jalview.org / jalview.git / blobdiff