Add GLprobs and MSAprobs to binaries

[jabaws.git] / binaries / src / MSAProbs-0.9.7 / MSAProbs / MSAGuideTree.h

diff --git a/binaries/src/MSAProbs-0.9.7/MSAProbs/MSAGuideTree.h b/binaries/src/MSAProbs-0.9.7/MSAProbs/MSAGuideTree.h
new file mode 100644 (file)
index 0000000..97d538a
--- /dev/null
+++ b/binaries/src/MSAProbs-0.9.7/MSAProbs/MSAGuideTree.h
@@ -0,0 +1,119 @@
+/***********************************************
+ * # Copyright 2009-2010. Liu Yongchao
+ * # Contact: Liu Yongchao, School of Computer Engineering,
+ * #                    Nanyang Technological University.
+ * # Emails:    liuy0039@ntu.edu.sg; nkcslyc@hotmail.com
+ * #
+ * # GPL version 3.0 applies.
+ * #
+ * ************************************************/
+
+#ifndef _MSA_GUIDE_TREE_H
+#define _MSA_GUIDE_TREE_H
+#include "MSADef.h"
+#include "MSA.h"
+
+#include "SafeVector.h"
+#include "MultiSequence.h"
+#include "ScoreType.h"
+#include "ProbabilisticModel.h"
+#include "SparseMatrix.h"
+
+class MSA;
+struct ValidNode {
+       ValidNode* prev;
+       ValidNode* next;
+       int n;                          //the index in the distance matrix                      
+       int node;                       //the index in the tree node entries
+};
+
+struct TreeNode {
+       struct TreeNode *left;                  //the pointer to its left child
+       struct TreeNode *right;                 //the pointer to its right child
+       struct TreeNode *parent;                //the pointer to its parent
+       int leftIdx;                                    //the index of the left child
+       int rightIdx;                                   //the index of the right child
+       int parentIdx;                                  //the index of its parent
+       int idx;                                                //the index of itself
+       float dist;                                             //the distance to its parent
+       int leaf;                                               //whether it is a leaf node or not
+       int order;                      //the number of generations dating back to its ancestor
+       int depth;                                              //the depth of the node
+};
+struct AlignmentOrder {
+       int nodeDepth;                  //the depth of the internal node
+       int leftOrder;                  //the order number of the right child
+       int rightOrder;                 //the order number of the left child
+       int* leftLeafs;                 //the indices of leafs in the left subtree
+       int leftNum;                    //the number of leafs in the left subtree
+       int* rightLeafs;                        //the indices of leafs in the right subtree
+       int rightNum;                   //the number of leafs in the right substree
+};
+
+class MSAGuideTree {
+public:
+       MSAGuideTree(MSA* msa, VVF& distMatrix, int numSeqs);
+       virtual ~MSAGuideTree() = 0;    //abstract class
+
+       //get the tree nodes
+       TreeNode* getNodes();
+       //get the leaf nodes
+       TreeNode* getLeafs();
+       //get the number of nodes;
+       int getNodesNum();
+       //get the number of leaf nodes
+       int getLeafsNum();
+       //get the root of the tree
+       TreeNode* getRoot() {
+               return this->root;
+       }
+       //get the alignment orders
+       AlignmentOrder* getAlignOrders();
+       int getAlignOrdersNum();
+       //construct the alignment orders
+       void createAlignmentOrders();
+
+       //construct the guide tree
+       virtual void create();
+       //calculate the sequence weights
+       virtual void getSeqsWeights();
+
+       /**********DEBUGING****************/
+       //display the tree
+       void displayTree();
+       //display the alignment orders
+       void displayAlignmentOrders();
+
+protected:
+       //join two nodes
+       void connectNodes(TreeNode* parent, int parentIdx, TreeNode* leftChild,
+                       float leftDist, TreeNode* rightChild, float rightDist);
+       //release the alignment orders vector
+       void releaseAlignmentOrders();
+       //recursive implemenation of constructing the alignment orders
+       int recursiveCreateAlignmentOrders(TreeNode* subRoot, int* subLeafs,
+                       int& subLeafsNum, int nodeDepth);
+
+       //system configurations
+       MSA* msa;
+       VVF* distMatrix;
+       int numSeqs;
+       int* seqsWeights;
+
+       //all the tree nodes
+       TreeNode* nodes;
+       int nodesNum;
+       int nodesSize;
+       //the root tree node
+       TreeNode* root;
+       //leaf node
+       TreeNode* leafs;
+       int leafsNum;
+
+       //alignment order
+       AlignmentOrder* alignOrders;
+       int alignOrdersNum;
+       int alignOrdersSize;
+};
+#endif
+