libshuff and updated help to include libshuff and modifications to read.dist.

[mothur.git] / fullmatrix.h

diff --git a/fullmatrix.h b/fullmatrix.h
index 389816abd70d40ce47ec324ce5d830bee77feff9..078cdb7699f53192b526ab3979036d5144b968e1 100644 (file)
--- a/fullmatrix.h
+++ b/fullmatrix.h
@@ -11,21 +11,57 @@
 
 #include "mothur.h"
 #include "groupmap.h"
+#include "globaldata.hpp"
+#include "progress.hpp"
+
+using namespace std;
+
+struct Names {
+       string          groupname;
+       string          seqName;
+};
+
+struct Swap {
+       int             a;
+       int             b;
+};
+
 
 class FullMatrix {
        
-public:
-       FullMatrix(){};
-       FullMatrix(ifstream&);
-       ~FullMatrix(){};
+       public:
+               FullMatrix(){};
+               FullMatrix(ifstream&);
+               ~FullMatrix(){};
        
-       int getNumSeqs();
+               int getNumSeqs();
+               void printMatrix(ostream&);
+               void setBounds();  //requires globaldata->Groups to be filled
+               vector<float> getMins(int); //returns vector of mins for "box" requested ie. groups A, B, 0 = AA, 1 = AB, 2 = BA, 3 = BB;
+               void getDist(vector<float>&);  //fills a vector with the valid distances for the integral form.
+               void shuffle(string, string);  //shuffles the sequences in the groups passed in.
+               void restore();  //unshuffles the matrix.
        
-private:
-       void sortGroups();  //this function sorts the sequences within the matrix.  
-       vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
-       GroupMap* groupmap;  //maps sequences to groups they belong to.
-       int numSeqs;
+       private:
+               void sortGroups(int, int);  //this function sorts the sequences within the matrix.
+               void getBounds(int&, string);
+               void readSquareMatrix(ifstream&);  
+               void readLTMatrix(ifstream&);
+               void printMinsForRows(ostream&);
+               
+               map<int, Names> index; // row in vector, sequence group.  need to know this so when we sort it can be updated.
+               map<int, Swap> restoreIndex; //a map of the swaps made so you can undo them in restore.
+               map<int, Names>::iterator it;
+               map<int, Swap>::reverse_iterator it2;
+                       
+               vector< vector<float> > matrix;  //a 2D distance matrix of all the sequences and their distances to eachother.
+               vector<float> minsForRows;  //vector< minimum distance for that subrow> - one for each comparison.
+               vector<int> bounds;  //bounds[1] = starting row in matrix from group B, bounds[2] = starting row in matrix from group C, bounds[3] = no need to find upper bound of C because its numSeqs.
+                                                               
+               GroupMap* groupmap;  //maps sequences to groups they belong to.
+               GlobalData* globaldata;
+               int numSeqs, numGroups, numUserGroups;
+               bool square;
 
 };