Clustering implementation for SILAC stuff. More...
#include <OpenMS/COMPARISON/CLUSTERING/SILACClustering.h>
Public Member Functions | |
SILACClustering (const PointCoordinate &cluster_dimension, DoubleReal rt_min, DoubleReal rt_max_spacing) | |
void | cluster () |
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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 |
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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... | |
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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 | |
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typedef DPosition< 2, DoubleReal > | PointCoordinate |
Coordinate of a point to be clustered. More... | |
typedef HashGrid< Cluster > | Grid |
The hash grid data type. More... | |
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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... | |
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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) |
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.
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inline |
void cluster | ( | ) |
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protected |
Join clusters with holes less then rt_max_spacing.
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protected |
Remove clusters smaller then rt_min.
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 |