binaries/src/muscle/clust.h

   1 #ifndef Clust_h\r
   2 #define Clust_h\r
   3 \r
   4 class Clust;\r
   5 class ClustNode;\r
   6 class ClustSet;\r
   7 class Phylip;\r
   8 class SortedNode;\r
   9 \r
  10 const unsigned RB_NIL = ((unsigned) 0xfff0);\r
  11 \r
  12 class ClustNode\r
  13         {\r
  14 public:\r
  15         ClustNode()\r
  16                 {\r
  17                 m_uIndex = uInsane;\r
  18                 m_uSize = uInsane;\r
  19                 m_dLength = (float) dInsane;\r
  20                 m_ptrLeft = 0;\r
  21                 m_ptrRight = 0;\r
  22                 m_ptrParent = 0;\r
  23                 m_ptrNextCluster = 0;\r
  24                 m_ptrPrevCluster = 0;\r
  25                 m_uLeafIndexes = 0;\r
  26                 }\r
  27         ~ClustNode()\r
  28                 {\r
  29                 delete[] m_uLeafIndexes;\r
  30                 }\r
  31         unsigned m_uIndex;\r
  32         unsigned m_uSize;\r
  33         float m_dLength;\r
  34         ClustNode *m_ptrLeft;\r
  35         ClustNode *m_ptrRight;\r
  36         ClustNode *m_ptrParent;\r
  37         ClustNode *m_ptrNextCluster;\r
  38         ClustNode *m_ptrPrevCluster;\r
  39         unsigned *m_uLeafIndexes;\r
  40         };\r
  41 \r
  42 class Clust\r
  43         {\r
  44 public:\r
  45         Clust();\r
  46         virtual ~Clust();\r
  47 \r
  48         void Create(ClustSet &Set, CLUSTER Method);\r
  49 \r
  50         unsigned GetLeafCount() const;\r
  51 \r
  52         unsigned GetClusterCount() const;\r
  53         unsigned GetClusterSize(unsigned uNodeIndex) const;\r
  54         unsigned GetLeaf(unsigned uClusterIndex, unsigned uLeafIndex) const;\r
  55 \r
  56         unsigned GetNodeCount() const { return 2*m_uLeafCount - 1; }\r
  57         const ClustNode &GetRoot() const { return m_Nodes[GetRootNodeIndex()]; }\r
  58         unsigned GetRootNodeIndex() const { return m_uNodeCount - 1; }\r
  59 \r
  60         const ClustNode &GetNode(unsigned uNodeIndex) const;\r
  61         bool IsLeaf(unsigned uNodeIndex) const;\r
  62         unsigned GetLeftIndex(unsigned uNodeIndex) const;\r
  63         unsigned GetRightIndex(unsigned uNodeIndex) const;\r
  64         float GetLength(unsigned uNodeIndex) const;\r
  65         float GetHeight(unsigned uNodeIndex) const;\r
  66         const char *GetNodeName(unsigned uNodeIndex) const;\r
  67         unsigned GetNodeId(unsigned uNodeIndex) const;\r
  68 \r
  69         JOIN GetJoinStyle() const { return m_JoinStyle; }\r
  70         LINKAGE GetCentroidStyle() const { return m_CentroidStyle; }\r
  71 \r
  72         void SetDist(unsigned uIndex1, unsigned uIndex2, float dDist);\r
  73         float GetDist(unsigned uIndex1, unsigned uIndex2) const;\r
  74 \r
  75         void ToPhylip(Phylip &tree);\r
  76 \r
  77         void LogMe() const;\r
  78 \r
  79 //private:\r
  80         void SetLeafCount(unsigned uLeafCount);\r
  81 \r
  82         void CreateCluster();\r
  83         void JoinNodes(unsigned uLeftNodeIndex, unsigned uRightNodeIndex, \r
  84           float dLeftLength, float dRightLength, unsigned uNewNodeIndex);\r
  85 \r
  86         void ChooseJoin(unsigned *ptruLeftIndex, unsigned *ptruRightIndex,\r
  87           float *ptrdLeftLength, float *ptrdRightLength);\r
  88         void ChooseJoinNeighborJoining(unsigned *ptruLeftIndex, unsigned *ptruRightIndex,\r
  89           float *ptrdLeftLength, float *ptrdRightLength);\r
  90         void ChooseJoinNearestNeighbor(unsigned *ptruLeftIndex, unsigned *ptruRightIndex,\r
  91           float *ptrdLeftLength, float *ptrdRightLength);\r
  92 \r
  93         float ComputeDist(unsigned uNewNodeIndex, unsigned uNodeIndex);\r
  94         float ComputeDistAverageLinkage(unsigned uNewNodeIndex, unsigned uNodeIndex);\r
  95         float ComputeDistMinLinkage(unsigned uNewNodeIndex, unsigned uNodeIndex);\r
  96         float ComputeDistMaxLinkage(unsigned uNewNodeIndex, unsigned uNodeIndex);\r
  97         float ComputeDistNeighborJoining(unsigned uNewNewIndex, unsigned uNodeIndex);\r
  98         float ComputeDistMAFFT(unsigned uNewNewIndex, unsigned uNodeIndex);\r
  99 \r
 100         float Calc_r(unsigned uNodeIndex) const;\r
 101 \r
 102         unsigned VectorIndex(unsigned uIndex1, unsigned uIndex2) const;\r
 103 \r
 104         unsigned GetFirstCluster() const;\r
 105         unsigned GetNextCluster(unsigned uNodeIndex) const;\r
 106 \r
 107         float ComputeMetric(unsigned uIndex1, unsigned uIndex2) const;\r
 108         float ComputeMetricNearestNeighbor(unsigned i, unsigned j) const;\r
 109         float ComputeMetricNeighborJoining(unsigned i, unsigned j) const;\r
 110 \r
 111         void InitMetric(unsigned uMaxNodeIndex);\r
 112         void InsertMetric(unsigned uIndex1, unsigned uIndex2, float dMetric);\r
 113         float GetMinMetric(unsigned *ptruIndex1, unsigned *ptruIndex2) const;\r
 114         float GetMinMetricBruteForce(unsigned *ptruIndex1, unsigned *ptruIndex2) const;\r
 115         void DeleteMetric(unsigned uIndex);\r
 116         void DeleteMetric(unsigned uIndex1, unsigned uIndex2);\r
 117         void ListMetric() const;\r
 118 \r
 119         void DeleteFromClusterList(unsigned uNodeIndex);\r
 120         void AddToClusterList(unsigned uNodeIndex);\r
 121 \r
 122         void RBDelete(unsigned RBNode);\r
 123         unsigned RBInsert(unsigned i, unsigned j, float fMetric);\r
 124 \r
 125         unsigned RBNext(unsigned RBNode) const;\r
 126         unsigned RBPrev(unsigned RBNode) const;\r
 127         unsigned RBMin(unsigned RBNode) const;\r
 128         unsigned RBMax(unsigned RBNode) const;\r
 129 \r
 130         void ValidateRB(const char szMsg[] = 0) const;\r
 131         void ValidateRBNode(unsigned Node, const char szMsg[]) const;\r
 132 \r
 133 //private:\r
 134         JOIN m_JoinStyle;\r
 135         LINKAGE m_CentroidStyle;\r
 136         ClustNode *m_Nodes;\r
 137         unsigned *m_ClusterIndexToNodeIndex;\r
 138         unsigned *m_NodeIndexToClusterIndex;\r
 139         unsigned m_uLeafCount;\r
 140         unsigned m_uNodeCount;\r
 141         unsigned m_uClusterCount;\r
 142         unsigned m_uTriangularMatrixSize;\r
 143         float *m_dDist;\r
 144         ClustSet *m_ptrSet;\r
 145         ClustNode *m_ptrClusterList;\r
 146         };\r
 147 \r
 148 #endif // Clust_h\r