massspec/clustering.h

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#ifndef _CLUSTERING_H_
#define _CLUSTERING_H_

/* Copyright (c) Kyriacos Leptos and the President and Fellows of Harvard University
   Release Date: 2004-11-01
   Part of the MapQuant suite library "massspec.lib" 
*/

typedef struct
{
        int                     vertex_1;
        int                     vertex_2;
        float           weight;
} Edge;

typedef Edge* EdgePointer;




Edge*                   EdgeArray_create(long nSize);
EdgePointer*    EdgePointerArray_create(long nSize);
Edge**                  EdgeTriangularMatrix_create(long nSize);
void                    EdgeTriangularMatrix_fprint(FILE* fp, Edge** matrix, long nSize);

int             Edge_cmpByWeight(const void *p1, const void *p2);
void    EdgeArray_sortByWeight(Edge* edges, long nEdges);

int             EdgePointer_cmpByWeight(const void *p1, const void *p2);
void    EdgePointerArray_sortByWeight(EdgePointer* edges, long nEdges);


typedef struct
{
        int                     vertex_1;
        int                     vertex_2;
        float           rt_weight;
        float           mz_weight;
} MEdge;

typedef MEdge* MEdgePointer;

MEdge*                  MEdgeArray_create(long nSize);
MEdgePointer*   MEdgePointerArray_create(long nSize);
MEdge**                 MEdgeTriangularMatrix_create(long nSize);
void                    MEdgeTriangularMatrix_fprint(FILE* fp, MEdge** matrix, long nSize);

int             MEdge_cmpByWeight(const void *p1, const void *p2);
void    MEdgeArray_sortByWeight(MEdge* edges, long nMEdges);

int             MEdgePointer_cmpByWeight(const void *p1, const void *p2);
void    MEdgePointerArray_sortByWeight(MEdgePointer* edges, long nMEdges);

struct Clusterer
{
        int       nLinkageType;
        float dLinkageRTThreshold;
        float dLinkageMZThreshold;
        float dAbundanceThreshold;
        int       nDimensions;
};

typedef struct Clusterer Clusterer;

void Clusterer_init(Clusterer* cl, float dRTThr, float dMZThr);


enum {CLUSTERING_SINGLE_LINK, CLUSTERING_AVERAGE_LINK, CLUSTERING_HYBRID_LINK};

void FPeak2iPointerSet_singleLinkageClustering(FPeak2iPointerSet* SET, Clusterer* clust);
void FPeak2iPointerSet_averageLinkageClustering(FPeak2iPointerSet* SET, Clusterer* clust);
void FPeak2iPointerSet_hybridLinkageClustering(FPeak2iPointerSet* SET, Clusterer* clust);
void FPeak2iPointerSet_cluster(FPeak2iPointerSet* SET, Clusterer* clust);



#endif

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