protocols::comparative_modeling::AlignmentCluster Class Reference

#include <AlignmentClustering.hh>

Public Member Functions
	AlignmentCluster (SequenceAlignment &aln_in)
virtual	~AlignmentCluster ()
void	add_aln (SequenceAlignment &aln_in)
SequenceAlignment	get_aln (Size index)
Real	size ()
SequenceAlignment	get_clusterCenter ()
void	output (std::ostream &alignment_out)
void	merge (AlignmentClusterOP cluster_in)
Real	overlap (AlignmentClusterOP cluster_in)

Private Attributes
vector1< SequenceAlignment >	alns

Constructor & Destructor Documentation

protocols::comparative_modeling::AlignmentCluster::AlignmentCluster

(

SequenceAlignment &

aln_in

)

Creates a AlignmentCluster

protocols::comparative_modeling::AlignmentCluster::~AlignmentCluster ( )

virtual

Deletes an AlignmentCluster object

References core::pose::Pose::clear().

Member Function Documentation

void protocols::comparative_modeling::AlignmentCluster::add_aln

(

SequenceAlignment &

aln_in

)

add alignment

SequenceAlignment protocols::comparative_modeling::AlignmentCluster::get_aln

(

Size

index

)

get aln

SequenceAlignment protocols::comparative_modeling::AlignmentCluster::get_clusterCenter

(

)

get cluster center – assumes lowest energy point

void protocols::comparative_modeling::AlignmentCluster::merge

(

AlignmentClusterOP

cluster_in

)

merges two clusters making sure the alignments are unique

References sequence, and core::sequence::SequenceAlignment::sequence().

void protocols::comparative_modeling::AlignmentCluster::output

(

std::ostream &

alignment_out

)

outputs cluster to file

References core::sequence::SequenceAlignment::printGrishinFormat(), sequence, and tr.

Real protocols::comparative_modeling::AlignmentCluster::overlap

(

AlignmentClusterOP

cluster_in

)

gets the percent of alignments in the input cluster that are in the current cluster

Real protocols::comparative_modeling::AlignmentCluster::size

(

)

get aln

Member Data Documentation

vector1<SequenceAlignment> protocols::comparative_modeling::AlignmentCluster::alns

private

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The documentation for this class was generated from the following files:

• src/protocols/comparative_modeling/AlignmentClustering.hh
• src/protocols/comparative_modeling/AlignmentClustering.cc