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protocols::comparative_modeling::AlignmentCluster Class Reference

#include <AlignmentClustering.hh>

Inheritance diagram for protocols::comparative_modeling::AlignmentCluster:
Inheritance graph
Collaboration diagram for protocols::comparative_modeling::AlignmentCluster:
Collaboration graph

Public Member Functions

 AlignmentCluster (SequenceAlignment &aln_in)
 Creates a AlignmentCluster More...
virtual ~AlignmentCluster ()
 Deletes an AlignmentCluster object More...
void add_aln (SequenceAlignment &aln_in)
 add alignment More...
SequenceAlignment get_aln (Size index)
 get aln More...
Real size ()
 get aln More...
SequenceAlignment get_clusterCenter ()
 get cluster center – assumes lowest energy point More...
void output (std::ostream &alignment_out)
 outputs cluster to file More...
void merge (AlignmentClusterOP cluster_in)
 merges two clusters making sure the alignments are unique More...
Real overlap (AlignmentClusterOP cluster_in)
 gets the percent of alignments in the input cluster that are in the current cluster More...

Private Attributes

vector1< SequenceAlignmentalns

Constructor & Destructor Documentation

protocols::comparative_modeling::AlignmentCluster::AlignmentCluster ( SequenceAlignment aln_in)

Creates a AlignmentCluster

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

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 core::sequence::SequenceAlignment::sequence().

void protocols::comparative_modeling::AlignmentCluster::output ( std::ostream &  alignment_out)

outputs cluster to file

References core::sequence::SequenceAlignment::printGrishinFormat(), 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

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