X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=tree.h;h=99cd68fa7f4b71dfeebffc90ad649a1f01c6564e;hb=2a7d1455e8cfe4f67a7173f3a7249762c5436217;hp=b6d5ea807a38801a872daf96b23557d53a241f4e;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6;p=mothur.git diff --git a/tree.h b/tree.h index b6d5ea8..99cd68f 100644 --- a/tree.h +++ b/tree.h @@ -13,6 +13,7 @@ #include "treenode.h" #include "globaldata.hpp" +class GlobalData; /* This class represents the treefile. */ class Tree { @@ -36,9 +37,10 @@ public: int findRoot(); //return index of root node //this function takes the leaf info and populates the non leaf nodes - void assembleTree(); + int assembleTree(); vector tree; //the first n nodes are the leaves, where n is the number of sequences. + private: GlobalData* globaldata; int numNodes, numLeaves; @@ -47,18 +49,25 @@ private: map::iterator it, it2; map mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children - map mergeGcounts(int); + + void addNamesToCounts(); void randomTopology(); void randomBlengths(); void randomLabels(vector); - void randomLabels(string, string); + //void randomLabels(string, string); void printBranch(int, ostream&, string); //recursively print out tree void parseTreeFile(); //parses through tree file to find names of nodes and number of them //this is required in case user has sequences in the names file that are //not included in the tree. //only takes names from the first tree in the tree file and assumes that all trees use the same names. - void readTreeString(ifstream&); + int readTreeString(ifstream&); + string readLabel(ifstream&); + string readName(ifstream&); + string readBranchLength(ifstream&); + + MothurOut* m; + }; #endif