4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
13 #include "../alignment/Alignment.h"
14 #include "AlignmentSteps.h"
23 void calcSeqWeights(int firstSeq, int lastSeq, vector<int>* sweight);
24 int readTree(Alignment* alignPtr, const string& treeFileName, int firstSeq,
26 auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
27 int calcSimilarities(Alignment* alignPtr, DistMatrix* distMat);
28 void clearTree(TreeNode* p);
33 void createTree(TreeNode* ptree, TreeNode* parent, ifstream* file);
34 void createNode(TreeNode* pptr, TreeNode* parent);
35 TreeNode* insertNode(TreeNode* pptr);
36 void clearTreeNodes(TreeNode* p);
37 TreeNode* reRoot(TreeNode* ptree, int nseqs);
38 TreeNode* insertRoot(TreeNode* p, float diff);
39 float calcRootMean(TreeNode* root, float *maxDist);
40 float calcMean(TreeNode* nptr, float *maxDist, int nSeqs);
42 int calcWeight(int leaf);
43 void skipSpace(ifstream* file);
44 void groupSeqs(TreeNode* p, int *nextGroups, int nSeqs, AlignmentSteps* stepsPtr);
45 void markGroup1(TreeNode* p, int *groups, int n);
46 void markGroup2(TreeNode* p, int *groups, int n);
48 void setInfo(TreeNode* p, TreeNode* parent, int pleaf, string pname, float
50 void debugPrintAllNodes(int nseqs);
53 AlignmentSteps progSteps;
68 const static int MAXERRS = 10;