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ConsensusInterval.java 683 (11 years ago) by duarte: Fixed bug: PhiPsiAverager was not working at all for single template case. Fixed bug: in ConsensusInterval changed MARGIN value to 2, for cases where max=min to make sure we pass an Interval bigger than 0 to tinker.
ConsensusSquare.java 662 (11 years ago) by duarte: Fixed bug: algorithm to find consensus was not working correctly. We weren't taking in account the 2-dimensionality of the problem. Changed the approach completely, new algorithm. Made the ConsensusInterval class a separate class and added new class ConsensusSquare to represent a phi/psi angle consensus region.
GraphAverager.java 759 (11 years ago) by duarte: Added printing of pairwise alignment when checkSequnces fail for target sequence
GraphAveragerError.java 688 (11 years ago) by duarte: Fixed bugs in averageGraph: - output of benchmark statistics and pairwise comparison was overlapping - benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes) Improved: - better handling of modes through mode variable that takes 1 of 3 states - better input check - in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph - changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph - now allowing alignments that contain other sequences than the target and the templates - new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match
PhiPsiAverager.java 811 (10 years ago) by duarte: New options -e and -i in reconstruct (for forcing angle constraints)
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