+++ /dev/null
-/**
- * Author: Mark Larkin
- *
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
- */
-/**
- * The SymMatrix class is used to store the distance matrix. It stores it in a double
- * array.
- * This class throws an out_of_range exception if we try to access an element outside
- * of the array bounds. It will throw a bad_alloc if we cannot allocate enough memory for
- * the distance matrix.
- */
-#ifndef SYMMATRIX_H
-#define SYMMATRIX_H
-
-#include<iostream>
-#include <vector>
-#include <iomanip>
-#include <cmath>
-#include <stdexcept>
-#include <new>
-#include <cstdlib>
-
-namespace clustalw
-{
-using namespace std;
-
-class SymMatrix
-{
- public:
- SymMatrix() : elements(0), numSeqs(0), subElements(0), firstSeq(0), numSeqsInSub(0){;}
- SymMatrix(int size)
- : elements(0),
- numSeqs(0),
- subElements(0),
- firstSeq(0),
- numSeqsInSub(0)
- {
- // Size is the numSeqs + 1
- numSeqs = size - 1;
- sizeElements = ((numSeqs + 1) * (numSeqs + 2)) >> 1;
- try
- {
- elements = new double[sizeElements];
- setAllArrayToVal(elements, sizeElements, 0.0);
- }
- catch(bad_alloc& e)
- {
- cout << "Could not allocate a distance matrix for " << numSeqs
- << " seqs.\n";
- throw e;
- }
-
- }
- ~SymMatrix()
- {
- if(elements)
- {
- delete [] elements;
- }
- if(subElements)
- {
- delete [] subElements;
- }
- }
-
- inline void SetAt(int nRow, int nCol, const double& value)
- {
- index = getIndex(nRow, nCol, numSeqs);
- elements[index] = value;
- }
-
- inline double GetAt(int nRow, int nCol)
- {
- index = getIndex(nRow, nCol, numSeqs);
- return elements[index];
- }
-
- inline void ResizeRect(int size, double val = 0.0)
- {
- numSeqs = size - 1;
- sizeElements = ((numSeqs + 1) * (numSeqs + 2)) >> 1;
- if(elements)
- {
- delete [] elements;
- }
- try
- {
- elements = new double[sizeElements];
- setAllArrayToVal(elements, sizeElements, val);
- }
- catch(bad_alloc& e)
- {
- cout << "Could not allocate a distance matrix for " << numSeqs
- << " seqs. Need to terminate program.\n";
- throw e;
- }
- }
-
- inline void setAllArrayToVal(double* array, int size, double val)
- {
- for(int i = 0; i < size; i++)
- {
- array[i] = val;
- }
- }
-
- inline int getSize()
- {
- return numSeqs + 1;
- }
-
- inline void clearArray()
- {
- sizeElements = 0;
- numSeqs = 0;
- if(elements)
- {
- delete [] elements;
- elements = 0;
- }
-
- numSeqsInSub = 0;
- sizeSubElements = 0;
-
- if(subElements)
- {
- delete [] subElements;
- subElements = 0;
- }
- }
-
- void printArray()
- {
- printArray(elements, sizeElements);
- }
-
- void printSubArray()
- {
- printArray(subElements, sizeSubElements);
- }
-
- void printArray(double* array, int size)
- {
- int numThisTime = 1;
- int numSoFar = 0;
- for(int i = 0; i < size; i++)
- {
-
- numSoFar++;
-
- if(numSoFar == numThisTime)
- {
- cout << " " << setw(4) << array[i] << "\n";
- numSoFar = 0;
- numThisTime++;
- }
- else
- {
- cout << " " << setw(4) << array[i];
- }
- }
- cout << "\n";
- }
-
- inline int getIndex(const int &i, const int &j, const int &nSeqs) const
- {
- if(i == 0 || j == 0)
- {
- return 0;
- }
-
- int _i = i - 1, _j = j - 1;
- if (_i == _j)
- {
- if ((_i >= nSeqs) || (_i < 0))
- {
- throw out_of_range("index out of range\n");
- }
- return (_i * (_i + 3)) >> 1;
- }
-
- if (_i > _j)
- {
- if ((_i >= nSeqs) || (_j < 0))
- {
- throw out_of_range("index out of range\n");
- }
- return ((_i * (_i + 1)) >> 1) + _j;
- }
-
- if ((_j >= nSeqs) || (_i < 0))
- {
- throw out_of_range("index out of range\n");
- }
- return ((_j * (_j + 1)) >> 1) + _i;
- }
-
- //inline
- inline double operator() (unsigned row, unsigned col) const
- {
- return elements[getIndex(row, col, numSeqs)];
- }
-
- inline double& operator() (unsigned row, unsigned col)
- {
- return elements[getIndex(row, col, numSeqs)];
- }
-
- inline double* getElements()
- {
- return elements;
- }
-
- inline double* getDistMatrix(int fSeq, int nSeqsInSub)
- {
- if(fSeq == 1 && numSeqs == nSeqsInSub)
- {
- return elements; // We want the whole array.
- }
- else
- {
- // Calculate the subMatrix and return it!!!
- try
- {
- if(subElements)
- {
- delete [] subElements;
- }
- sizeSubElements = ((nSeqsInSub + 1) * (nSeqsInSub + 2)) >> 1;
- numSeqsInSub = nSeqsInSub;
-
- subElements = new double[sizeSubElements];
- setAllArrayToVal(subElements, sizeSubElements, 0.0);
-
- int currIndex = 0;
- subElements[0] = 0.0;
- int lSeq = fSeq + numSeqsInSub - 1; // NOTE this is wrong!!!!! Need to fix
-
- for(int i = fSeq; i <= lSeq; i++)
- {
- for(int j = i + 1; j <= lSeq; j++)
- {
- currIndex = getIndex(i - fSeq + 1, j - fSeq + 1, numSeqsInSub);
- subElements[currIndex] = elements[getIndex(i, j, numSeqs)];
- }
- }
-
- return subElements;
- }
- catch(bad_alloc& e)
- {
- cout << "Out of Memory!\n";
- throw e;
- }
- }
- }
-
- void clearSubArray()
- {
- if(subElements)
- {
- delete [] subElements;
- }
- subElements = 0;
- sizeSubElements = 0;
- numSeqsInSub = 0;
- }
-
- void makeSimilarityMatrix()
- {
- double value;
- for (int i = 0; i < numSeqs; i++)
- {
- SetAt(i + 1, i + 1, 0.0);
- for (int j = 0; j < i; j++)
- {
- value = 100.0 - (GetAt(i + 1, j + 1)) * 100.0;
- SetAt(i + 1, j + 1, value);
- //distMat->SetAt(j + 1, i + 1, value);
- }
- }
- }
-
- private:
- double* elements;
- int sizeElements;
- int numSeqs;
- int index;
- double* subElements; // To be used to return a sub matrix.
- int firstSeq, numSeqsInSub;
- int sizeSubElements;
-};
-
-}
-
-#endif
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