X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fmarkdown%2Freleases%2Frelease-2_7.md;fp=help%2Fmarkdown%2Freleases%2Frelease-2_7.md;h=40a6a2ac266598d9612dfa88f845d8d3009a1e73;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=0000000000000000000000000000000000000000;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git diff --git a/help/markdown/releases/release-2_7.md b/help/markdown/releases/release-2_7.md new file mode 100644 index 0000000..40a6a2a --- /dev/null +++ b/help/markdown/releases/release-2_7.md @@ -0,0 +1,135 @@ +--- +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 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