--- 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