JAL-4004 existing releases-VERSION.md files and releases.html template

[jalview.git] / help / markdown / releases / release-2_6.md

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+---
+channel: release
+version: 2.6
+date: 2010-09-26
+---
+
+## New Features
+
+
+
+### Application
+- Support for **Ja**va **b**ioinformatics **a**nalysis **w**eb **s**ervices (JABAWS)
+- Web Services preference tab
+- Analysis parameters dialog box and user defined preferences
+- Improved speed and layout of Envision2 service menu
+- Superpose structures using associated sequence alignment
+- Export coordinates and projection as CSV from PCA viewer
+
+
+### Applet
+- enable javascript: execution by the applet via the link out mechanism
+
+
+### Other
+- Updated the Jmol Jalview interface to work with Jmol series 12
+- The Jalview Desktop and JalviewLite applet now require Java 1.5
+- Allow Jalview feature colour specification for GFF sequence annotation files
+- New 'colour by label' keword in Jalview feature file type colour specification
+- New Jalview Desktop Groovy API method that allows a script to check if it being run in an interactive session or in a batch operation from the Jalview command line
+
+
+## Issues Resolved
+
+- clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column
+
+
+### Application
+- typo in AlignmentFrame->View->Hide->all but selected Regions menu item
+- sequence fetcher replaces ',' for ';' when the ',' is part of a valid accession ID
+- fatal OOM if object retrieved by sequence fetcher runs out of memory
+- unhandled Out of Memory Error when viewing pca analysis results
+- InstallAnywhere builds fail to launch on OS X java 10.5 update 4 (due to apple Java 1.6 update)
+- Installanywhere Jalview silently fails to launch
+
+
+### Applet
+- Jalview.getFeatureGroups() raises an ArrayIndexOutOfBoundsException if no feature groups are defined.