--- /dev/null
+---
+channel: release
+version: 2.5.1
+date: 2010-06-14
+---
+
+## Issues Resolved
+
+- Alignment prettyprinter doesn't cope with long sequence IDs
+- clustalx colourscheme colours Ds preferentially when both D+E are present in over 50% of the column
+- nucleic acid structures retrieved from PDB do not import correctly
+- More columns get selected than were clicked on when a number of columns are hidden
+- annotation label popup menu not providing correct add/hide/show options when rows are hidden or none are present
+- Stockholm format shown in list of readable formats, and parser copes better with alignments from RFAM.
+- CSV output of consensus only includes the percentage of all symbols if sequence logo display is enabled
+
+
+### Applet
+- annotation panel disappears when annotation is hidden/removed
+
+
+### Application
+- Alignment view not redrawn properly when new alignment opened where annotation panel is visible but no annotations are present on alignment
+- pasted region containing hidden columns is incorrectly displayed in new alignment window
+- Jalview slow to complete operations when stdout is flooded (fix is to close the Jalview console)
+- typo in AlignmentFrame->View->Hide->all but selected Rregions menu item.
+- inconsistent group submenu and Format submenu entry 'Un' or 'Non'conserved
+- Sequence feature settings are being shared by multiple distinct alignments
+- group annotation not recreated when tree partition is changed
+- double click on group annotation to select sequences does not propagate to associated trees
+- Mac OSX specific issues:
+ - exception raised when mouse clicked on desktop window background
+ - Desktop menu placed on menu bar and application name set correctly
+ - sequence feature settings not wide enough for the save feature colourscheme button
git://source.jalview.org / jalview.git / blobdiff