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Author: duarte
Date: Tue Jan 15 13:19:36 2008 UTC (14 years, 8 months ago)
Log Message:
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this. 
NOTE: graph averaging hasn't been tested after the change

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