Changes between Initial Version and Version 1 of Ticket #4678, comment 1


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Timestamp:
May 21, 2021, 10:12:05 AM (4 years ago)
Author:
pett

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  • Ticket #4678, comment 1

    initial v1  
    11I guess the first question is what were you trying to get done by opening this large alignment?  There might be better or more direct means we could implement to get what you needed done than via the alignment.
    22
    3 When I ported the viewer to ChimeraX I wanted the same capabilities as in Chimera, and two of those capabilities were individual alignment letter coloring and tooltips (showing structure association info).  This means that each letter in the alignment is its own graphics item.  Once the port was well underway and initial versions of the viewer were available, Elaine said she preferred black lettering for the alignment sequences.  Removing the individual color requirement means that if I change to a slightly uglier fixed-width font I could layout the sequences in large text blocks, which would be far more efficient.  I would have to handle the tooltips in a far more manual fashion to show the per-letter association, and rework the quite complicated layout machinery, it I would like better performance.
     3When I ported the viewer to ChimeraX I wanted the same capabilities as in Chimera, and two of those capabilities were individual alignment letter coloring and tooltips (showing structure association info).  This means that each letter in the alignment is its own graphics item.  Once the port was well underway and initial versions of the viewer were available, Elaine said she preferred black lettering for the alignment sequences.  Removing the individual color requirement means that if I change to a slightly uglier fixed-width font I could layout the sequences in large text blocks, which would be far more efficient.  I would have to handle the tooltips in a far more manual fashion to show the per-letter association, and rework the quite complicated layout machinery, but I would like better performance.
    44
    55Alternatively, it may just be better and more informative to use Profile Grids for large alignments.