Merge branch 'long-align'

Conflicts:
	src/Algorithm/Makefile.am
	src/Util/Makefile.am

src/Algorithm/ExtensionDP.h

@@ -0,0 +1,125 @@
+///----------------------------------------------
+// Copyright 2011 Wellcome Trust Sanger Institute
+// Written by Jared Simpson (js18@sanger.ac.uk)
+// Released under the GPL
+//-----------------------------------------------
+//
+//
+// ExtensionDP - Class implementing an iterative
+// dynamic programming alignment. The alignment
+// starts by globally constructing an alignment
+// between two strings in a seed region. This initial
+// alignment can then be extended row-by-row as one of the
+// strings is extended. This is the core data structure for the 
+// StringThreader class
+// 
+#ifndef EXTENSION_DP_H
+#define EXTENSION_DP_H
+
+#include <vector>
+#include "StdAlnTools.h"
+
+// Structure holding the score for a single cell
+// of the DP matrix
+struct DPCell
+{
+    DPCell() : score(0), ctype('\0') {}
+    int score;
+    char ctype;
+};
+typedef std::vector<DPCell> CellVector;
+
+// Result object providing the coordinates
+// of the endpoints of the alignment
+struct ExtensionDPAlignment
+{
+    int query_align_length;
+    int target_align_length;
+};
+
+// Core class providing a single column of the dynamic
+// programming matrix
+class BandedDPColumn
+{
+    public:
+
+        //
+        // Functions
+        //
+        BandedDPColumn(int ci, int maxRows, int bandwidth, const BandedDPColumn* prevColumn);
+
+        // Simple getters
+        int getColIdx() const { return m_colIdx; }
+        int getBandwidth() const { return m_bandwidth; }
+
+        int getRowScore(int row) const;
+        char getRowType(int row) const;
+        int getCellScore(int colIdx, int rowIdx) const;
+        int getMinRow() const { return m_rowStartIdx; }   
+        int getMaxRow() const { return m_rowEndIdx; }
+        const BandedDPColumn* getPreviousColumn() const;
+
+        // Set the cell information for a given row in the column
+        void setRowScore(int row, int score, char ctype);
+
+        // Returns the row index of the best scoring cell
+        int getBestRowIndex() const;
+
+        // Calculate and set the score for the row
+        void fillRowEditDistance(int rowIdx, int matchScore);
+
+    private:
+
+        //
+        // Functions
+        //
+        int getVectorIndex(int rowIdx) const;
+
+        //
+        // Data
+        //
+        int m_colIdx;
+        int m_maxRows;
+        int m_rowStartIdx;
+        int m_rowEndIdx;
+        int m_bandwidth;
+        CellVector m_cells;
+        const BandedDPColumn* m_pPrevColumn;
+};
+typedef std::vector<BandedDPColumn*> BandedDPColumnPtrVector;
+
+// Algorithms to use/extend the extensionDP functionality
+namespace ExtensionDP
+{
+    // Initialize the extension DP by computing a global alignment between extendable and fixed
+    // This function allocates memory and stores the created pointers in outPtrVec
+    void createInitialAlignment(const std::string& extendable, const std::string& fixed, int bandwidth, BandedDPColumnPtrVector& outPtrVec);
+
+    // Create a new column, representing the extended alignment from pPrevColumn to char b
+    BandedDPColumn* createNewColumn(char b, const std::string& fixed, const BandedDPColumn* pPrevColumn);
+
+    // Calculate the best alignment through the matrix. Assumes that
+    // path_t* is pre-allocated with maxPathLength entries.
+    void backtrack(const BandedDPColumn* pLastColumn, path_t* path, int* pPathLen, const int maxPathLength);
+
+    // Check if the extension has terminated. This is true if there are more
+    // than insertionThreshold insertions at the end of the alignment.
+    bool isExtensionTerminated(const BandedDPColumn* pLastColumn, int insertionThreshold);
+
+    // Return the best trimmed alignment of the extensionDP object requiring minMatches matches
+    // at the end of the alignment
+    ExtensionDPAlignment findTrimmedAlignment(const BandedDPColumn* pLastColumn, int minMatches);
+
+    // Calculate mismatch/error rates between the query and the string up to pStartColumn
+    double calculateLocalEditPercentage(const BandedDPColumn* pStartColumn, int numBases);
+    double calculateGlobalEditPercentage(const BandedDPColumn* pStartColumn);
+    void countEditsAndAlignLength(const BandedDPColumn* pStartColumn, int& edits, int& alignLength);
+
+    // Print the alignment starting from the given column
+    void printAlignment(const std::string& s1, const std::string& s2, const BandedDPColumn* pLastColumn);
+
+    // Print the full scoring matrix
+    void printMatrix(const BandedDPColumnPtrVector& columnPtrVec);
+};
+
+#endif