 ../
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PhiPsiAverager.java
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810
(13 years ago)
by duarte:
Two new statics: to get phi/psi constraints for intervals of one given structure.
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GraphAverager.java
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759
(13 years ago)
by duarte:
Added printing of pairwise alignment when checkSequnces fail for target sequence
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GraphAveragerError.java
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688
(13 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
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ConsensusInterval.java
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683
(14 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.
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ConsensusSquare.java
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662
(14 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.
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