Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / clust.h

diff --git a/website/archive/binaries/mac/src/muscle/clust.h b/website/archive/binaries/mac/src/muscle/clust.h
deleted file mode 100644 (file)
index 4d86af6..0000000
--- a/website/archive/binaries/mac/src/muscle/clust.h
+++ /dev/null
@@ -1,148 +0,0 @@
-#ifndef Clust_h\r
-#define Clust_h\r
-\r
-class Clust;\r
-class ClustNode;\r
-class ClustSet;\r
-class Phylip;\r
-class SortedNode;\r
-\r
-const unsigned RB_NIL = ((unsigned) 0xfff0);\r
-\r
-class ClustNode\r
-       {\r
-public:\r
-       ClustNode()\r
-               {\r
-               m_uIndex = uInsane;\r
-               m_uSize = uInsane;\r
-               m_dLength = (float) dInsane;\r
-               m_ptrLeft = 0;\r
-               m_ptrRight = 0;\r
-               m_ptrParent = 0;\r
-               m_ptrNextCluster = 0;\r
-               m_ptrPrevCluster = 0;\r
-               m_uLeafIndexes = 0;\r
-               }\r
-       ~ClustNode()\r
-               {\r
-               delete[] m_uLeafIndexes;\r
-               }\r
-       unsigned m_uIndex;\r
-       unsigned m_uSize;\r
-       float m_dLength;\r
-       ClustNode *m_ptrLeft;\r
-       ClustNode *m_ptrRight;\r
-       ClustNode *m_ptrParent;\r
-       ClustNode *m_ptrNextCluster;\r
-       ClustNode *m_ptrPrevCluster;\r
-       unsigned *m_uLeafIndexes;\r
-       };\r
-\r
-class Clust\r
-       {\r
-public:\r
-       Clust();\r
-       virtual ~Clust();\r
-\r
-       void Create(ClustSet &Set, CLUSTER Method);\r
-\r
-       unsigned GetLeafCount() const;\r
-\r
-       unsigned GetClusterCount() const;\r
-       unsigned GetClusterSize(unsigned uNodeIndex) const;\r
-       unsigned GetLeaf(unsigned uClusterIndex, unsigned uLeafIndex) const;\r
-\r
-       unsigned GetNodeCount() const { return 2*m_uLeafCount - 1; }\r
-       const ClustNode &GetRoot() const { return m_Nodes[GetRootNodeIndex()]; }\r
-       unsigned GetRootNodeIndex() const { return m_uNodeCount - 1; }\r
-\r
-       const ClustNode &GetNode(unsigned uNodeIndex) const;\r
-       bool IsLeaf(unsigned uNodeIndex) const;\r
-       unsigned GetLeftIndex(unsigned uNodeIndex) const;\r
-       unsigned GetRightIndex(unsigned uNodeIndex) const;\r
-       float GetLength(unsigned uNodeIndex) const;\r
-       float GetHeight(unsigned uNodeIndex) const;\r
-       const char *GetNodeName(unsigned uNodeIndex) const;\r
-       unsigned GetNodeId(unsigned uNodeIndex) const;\r
-\r
-       JOIN GetJoinStyle() const { return m_JoinStyle; }\r
-       LINKAGE GetCentroidStyle() const { return m_CentroidStyle; }\r
-\r
-       void SetDist(unsigned uIndex1, unsigned uIndex2, float dDist);\r
-       float GetDist(unsigned uIndex1, unsigned uIndex2) const;\r
-\r
-       void ToPhylip(Phylip &tree);\r
-\r
-       void LogMe() const;\r
-\r
-//private:\r
-       void SetLeafCount(unsigned uLeafCount);\r
-\r
-       void CreateCluster();\r
-       void JoinNodes(unsigned uLeftNodeIndex, unsigned uRightNodeIndex, \r
-         float dLeftLength, float dRightLength, unsigned uNewNodeIndex);\r
-\r
-       void ChooseJoin(unsigned *ptruLeftIndex, unsigned *ptruRightIndex,\r
-         float *ptrdLeftLength, float *ptrdRightLength);\r
-       void ChooseJoinNeighborJoining(unsigned *ptruLeftIndex, unsigned *ptruRightIndex,\r
-         float *ptrdLeftLength, float *ptrdRightLength);\r
-       void ChooseJoinNearestNeighbor(unsigned *ptruLeftIndex, unsigned *ptruRightIndex,\r
-         float *ptrdLeftLength, float *ptrdRightLength);\r
-\r
-       float ComputeDist(unsigned uNewNodeIndex, unsigned uNodeIndex);\r
-       float ComputeDistAverageLinkage(unsigned uNewNodeIndex, unsigned uNodeIndex);\r
-       float ComputeDistMinLinkage(unsigned uNewNodeIndex, unsigned uNodeIndex);\r
-       float ComputeDistMaxLinkage(unsigned uNewNodeIndex, unsigned uNodeIndex);\r
-       float ComputeDistNeighborJoining(unsigned uNewNewIndex, unsigned uNodeIndex);\r
-       float ComputeDistMAFFT(unsigned uNewNewIndex, unsigned uNodeIndex);\r
-\r
-       float Calc_r(unsigned uNodeIndex) const;\r
-\r
-       unsigned VectorIndex(unsigned uIndex1, unsigned uIndex2) const;\r
-\r
-       unsigned GetFirstCluster() const;\r
-       unsigned GetNextCluster(unsigned uNodeIndex) const;\r
-\r
-       float ComputeMetric(unsigned uIndex1, unsigned uIndex2) const;\r
-       float ComputeMetricNearestNeighbor(unsigned i, unsigned j) const;\r
-       float ComputeMetricNeighborJoining(unsigned i, unsigned j) const;\r
-\r
-       void InitMetric(unsigned uMaxNodeIndex);\r
-       void InsertMetric(unsigned uIndex1, unsigned uIndex2, float dMetric);\r
-       float GetMinMetric(unsigned *ptruIndex1, unsigned *ptruIndex2) const;\r
-       float GetMinMetricBruteForce(unsigned *ptruIndex1, unsigned *ptruIndex2) const;\r
-       void DeleteMetric(unsigned uIndex);\r
-       void DeleteMetric(unsigned uIndex1, unsigned uIndex2);\r
-       void ListMetric() const;\r
-\r
-       void DeleteFromClusterList(unsigned uNodeIndex);\r
-       void AddToClusterList(unsigned uNodeIndex);\r
-\r
-       void RBDelete(unsigned RBNode);\r
-       unsigned RBInsert(unsigned i, unsigned j, float fMetric);\r
-\r
-       unsigned RBNext(unsigned RBNode) const;\r
-       unsigned RBPrev(unsigned RBNode) const;\r
-       unsigned RBMin(unsigned RBNode) const;\r
-       unsigned RBMax(unsigned RBNode) const;\r
-\r
-       void ValidateRB(const char szMsg[] = 0) const;\r
-       void ValidateRBNode(unsigned Node, const char szMsg[]) const;\r
-\r
-//private:\r
-       JOIN m_JoinStyle;\r
-       LINKAGE m_CentroidStyle;\r
-       ClustNode *m_Nodes;\r
-       unsigned *m_ClusterIndexToNodeIndex;\r
-       unsigned *m_NodeIndexToClusterIndex;\r
-       unsigned m_uLeafCount;\r
-       unsigned m_uNodeCount;\r
-       unsigned m_uClusterCount;\r
-       unsigned m_uTriangularMatrixSize;\r
-       float *m_dDist;\r
-       ClustSet *m_ptrSet;\r
-       ClustNode *m_ptrClusterList;\r
-       };\r
-\r
-#endif // Clust_h\r