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SILACClustering Class Reference

Clustering implementation for SILAC stuff. More...

#include <OpenMS/COMPARISON/CLUSTERING/SILACClustering.h>

Inheritance diagram for SILACClustering:
HierarchicalClustering< SILACPattern * >

Public Member Functions

 SILACClustering (const PointCoordinate &cluster_dimension, DoubleReal rt_min, DoubleReal rt_max_spacing)
 
void cluster ()
 
- Public Member Functions inherited from HierarchicalClustering< SILACPattern * >
 HierarchicalClustering (const PointCoordinate &cluster_dimension)
 Constructor. More...
 
Grid::cell_iterator insertPoint (const PointCoordinate &d, const SILACPattern *&ref)
 Insert new PointCoordinate into grid. More...
 
void cluster ()
 Perform clustering of all existing points. More...
 

Public Attributes

const DoubleReal rt_min
 
const DoubleReal rt_max_spacing
 
- Public Attributes inherited from HierarchicalClustering< SILACPattern * >
Grid grid
 The hash grid. More...
 

Protected Member Functions

void removeSmall_ ()
 Remove clusters smaller then rt_min. More...
 
void joinLarge_ ()
 Join clusters with holes less then rt_max_spacing. More...
 
- Protected Member Functions inherited from HierarchicalClustering< SILACPattern * >
Grid::cell_iterator insertCluster_ (const P &p)
 Insert new Cluster into grid. More...
 
void clusterIndex_ (const typename Grid::CellIndex &p)
 Perform clustering at given cell index. More...
 
void gridCells5x5_ (typename Grid::CellIndex cur, ClusterCells &cells)
 Collect all cells used to cluster at given cell index. More...
 
void gridCell_ (const typename Grid::CellIndex &cur, ClusterCells &cells, bool center=false, bool ignore_missing=true)
 Collect one cell. More...
 
void addTreeDistance_ (TreeNode *tree, ClusterTrees &trees, TreeDistanceQueue &dists)
 Add a new tree to the set of trees and distance queue. More...
 
DoubleReal treeDistance_ (TreeNode *left, TreeNode *right)
 Returns distance of two tree nodes Returns the euclidean distance of the coordinates of the two trees. It checks the size of the bounding box and returns INFINITY if it gets to large. More...
 
void tree2Cluster_ (const TreeNode *tree, Cluster &cluster)
 Recursively add the points of a finished cluster into the hash grid. All points are saved in the leafs of the tree. More...
 
void tree2Points_ (const TreeNode *tree)
 Recursively add the points of an unfinished cluster back to the grid. All points are saved in the leafs of the tree. More...
 

Additional Inherited Members

- Public Types inherited from HierarchicalClustering< SILACPattern * >
typedef DPosition< 2, DoubleRealPointCoordinate
 Coordinate of a point to be clustered. More...
 
typedef HashGrid< Cluster > Grid
 The hash grid data type. More...
 
- Protected Types inherited from HierarchicalClustering< SILACPattern * >
typedef std::map< typename
Grid::CellIndex, std::pair
< typename Grid::CellContent
*, bool > > 
ClusterCells
 
typedef boost::unordered_set
< TreeNode * > 
ClusterTrees
 
typedef std::priority_queue
< TreeDistance, std::vector
< TreeDistance >, std::greater
< TreeDistance > > 
TreeDistanceQueue
 Priority queue queue used to find minimum distances. More...
 
- Static Protected Member Functions inherited from HierarchicalClustering< SILACPattern * >
static PointCoordinate coordScalarDiv_ (const PointCoordinate &lhs, const DoubleReal &rhs)
 
static PointCoordinate coordElemDiv_ (const PointCoordinate &lhs, const PointCoordinate &rhs)
 
static bool coordElemGreater_ (const PointCoordinate &lhs, const PointCoordinate &rhs)
 
static DoubleReal coordDist_ (const PointCoordinate &lhs, const PointCoordinate &rhs)
 

Detailed Description

Clustering implementation for SILAC stuff.

It cleans up the results of the hierarchical clustering for the search of labeled and unlabeled peptide data. It removes too small clusters and joins clusters with small gaps that the clustering split on purpose.

Warning
The cleanups will not work on random data

Constructor & Destructor Documentation

SILACClustering ( const PointCoordinate cluster_dimension,
DoubleReal  rt_min,
DoubleReal  rt_max_spacing 
)
inline

Member Function Documentation

void cluster ( )
void joinLarge_ ( )
protected

Join clusters with holes less then rt_max_spacing.

void removeSmall_ ( )
protected

Remove clusters smaller then rt_min.

Member Data Documentation

const DoubleReal rt_max_spacing
const DoubleReal rt_min

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5