JAL-1677 allowed splitFrames to be saved/restored to the project, but currently, when a splitFrame is restored, its desktop X,Y appears to be based on the default 'new window' position (just below and to the right of the last newly displayed alignment window). Ideally, the splitFrame X,Y position should be saved and faithfully restored (with scaling/relocation according to desktop geometry changes) like any other first-class window in the Jalview desktop.
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JAL-1916window position not preserved after moving window with gathered views
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JAL-1915Vertical scroll position not restored from Jalview project
Open
JAL-1677Save and restore SplitFrame view to/from Jalview project