ngs_server 0.1 → 0.2

data/ext/vcftools/cpp/.svn/text-base/dgeev.cpp.svn-base

@@ -0,0 +1,146 @@
+/*
+ * dgeev.cpp
+ *
+ *	Created on: 20 Apr 2011
+ *			Author: auton
+ * ($Revision: 1 $)
+ */
+
+#include "dgeev.h"
+
+void dgeev_sort(double *Er, double *Ei, int N)
+{
+	double temp, *E2;
+	int i, j;
+
+	E2 = new double[N];
+	for (i=0; i<N; i++)
+		E2[i] = Er[i]*Er[i]+Ei[i]*Ei[i];
+
+	for (j=0; j<N; j++)
+		for (i=0; i<N-1; i++)
+			if (fabs(E2[i])<fabs(E2[i+1]))
+			{
+				temp = E2[i]; E2[i] = E2[i+1]; E2[i+1] = temp;
+				temp = Er[i]; Er[i] = Er[i+1]; Er[i+1] = temp;
+				temp = Ei[i]; Ei[i] = Ei[i+1]; Ei[i+1] = temp;
+			}
+
+	delete [] E2;
+}
+
+
+void dgeev_sort(double *Er, double *Ei, double **Evecs, int N)
+{
+	double temp, *E2;
+	int i, j, k;
+
+	E2 = new double[N];
+	for (i=0; i<N; i++)
+		E2[i] = Er[i]*Er[i]+Ei[i]*Ei[i];
+
+	for (j=0; j<N; j++)
+		for (i=0; i<N-1; i++)
+			if (fabs(E2[i])<fabs(E2[i+1]))
+			{
+				temp = E2[i]; E2[i] = E2[i+1]; E2[i+1] = temp;
+				temp = Er[i]; Er[i] = Er[i+1]; Er[i+1] = temp;
+				temp = Ei[i]; Ei[i] = Ei[i+1]; Ei[i+1] = temp;
+
+				for (k=0; k<N; k++)
+				{
+					temp = Evecs[k][i];
+					Evecs[k][i] = Evecs[k][i+1];
+					Evecs[k][i+1] = temp;
+				}
+			}
+
+	delete [] E2;
+}
+
+
+double* dgeev_ctof(double **in, int rows, int cols)
+{
+	double *out;
+	int i, j;
+
+	out = new double[rows*cols];
+	for (i=0; i<rows; i++)
+		for (j=0; j<cols; j++)
+			out[i+j*cols] = in[i][j];
+	return(out);
+}
+
+
+void dgeev_ftoc(double *in, double **out, int rows, int cols)
+{
+	int i, j;
+
+	for (i=0; i<rows; i++)
+		for (j=0; j<cols; j++)
+			out[i][j] = in[i+j*cols];
+}
+
+
+void dgeev(double **H, int n, double *Er, double *Ei)
+{
+	char jobvl, jobvr;
+	int lda, ldvl, ldvr, lwork, info;
+	double *a, *vl, *vr, *work;
+
+	jobvl = 'N'; // V/N to calculate/not calculate the left eigenvectors of the matrix H.
+	jobvr = 'N'; // As above, but for the right eigenvectors.
+
+	lda = n; // The leading dimension of the matrix a.
+	a = dgeev_ctof(H, n, lda); // Convert the matrix H from double pointer C form to single pointer Fortran form.
+
+	/* Whether we want them or not, we need to define the matrices
+		 for the eigenvectors, and give their leading dimensions.
+		 We also create a vector for work space. */
+
+	ldvl = n;
+	vl = new double[n*n];
+	ldvr = n;
+	vr = new double[n*n];
+	work = new double[4*n];
+	lwork = 4*n;
+
+	dgeev_(&jobvl, &jobvr, &n, a, &lda, Er, Ei, vl, &ldvl, vr, &ldvr, work, &lwork, &info);
+
+	dgeev_sort(Er, Ei, n); //Sort the results by eigenvalue in decreasing magnitude.
+
+	delete [] a;
+	delete [] vl;
+	delete [] vr;
+	delete [] work;
+}
+
+
+void dgeev(double **H, int n, double *Er, double *Ei, double **Evecs)
+{
+	char jobvl, jobvr;
+	int lda,	ldvl, ldvr, lwork, info;
+	double *a, *vl, *vr, *work;
+
+	jobvl = 'N';
+	jobvr = 'V';
+	lda = n;
+	a = dgeev_ctof(H, n, lda);
+
+	ldvl = n;
+	vl = new double[n*n];
+	ldvr = n;
+	vr = new double[n*n];
+	work = new double[4*n];
+	lwork = 4*n;
+
+	dgeev_(&jobvl, &jobvr, &n, a, &lda, Er, Ei, vl, &ldvl, vr, &ldvr, work, &lwork, &info);
+
+	dgeev_ftoc(vr, Evecs, n, ldvr);
+	dgeev_sort(Er, Ei, Evecs, n);
+
+	delete [] a;
+	delete [] vl;
+	delete [] vr;
+	delete [] work;
+}

data/ext/vcftools/cpp/.svn/text-base/dgeev.h.svn-base

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+/*
+ * dgeev.h
+ * ($Revision: 1 $)
+  This file contains a wrapper around the LAPACK dgeev routine,
+  used to calculate eigenvalues and associated eigenvectors
+  for a square asymmetric matrix H. Since the matrix is asymmetrix,
+  both real and imaginary components of the eigenvalues are returned.
+  For real, symmetric matricies, the eigenvalues will be real, and
+  hence the complex terms equal to zero.
+
+  There are two function calls defined in this header, of the
+  forms
+
+    void dgeev(double **H, int n, double *Er, double *Ei)
+    void dgeev(double **H, int n, double *Er, double *Ei, double **Evecs)
+
+    H: the n by n matrix that we are solving.
+    n: the order of the square matrix H.
+    Er: an n-element array to hold the real parts of the eigenvalues.
+    Ei: an n-element array to hold the imaginary parts of the eigenvalues.
+    Evecs: an n by n matrix to hold the eigenvectors.
+*/
+
+#ifndef DGEEV_H_
+#define DGEEV_H_
+
+#include <cmath>
+
+void dgeev(double **H, int n, double *Er, double *Ei);
+void dgeev(double **H, int n, double *Er, double *Ei, double **Evecs);
+
+double *dgeev_ctof(double **in, int rows, int cols);
+void dgeev_ftoc(double *in, double **out, int rows, int cols);
+void dgeev_sort(double *Er, double *Ei, int N);
+void dgeev_sort(double *Er, double *Ei, double **Evecs, int N);
+
+ 
+extern "C" void dgeev_(char *jobvl, char *jobvr, int *n, double *a,
+		       int *lda, double *wr, double *wi, double *vl,
+		       int *ldvl, double *vr, int *ldvr,
+		       double *work, int *lwork, int *info);
+
+#endif

data/ext/vcftools/cpp/.svn/text-base/output_log.cpp.svn-base

@@ -0,0 +1,79 @@
+/*
+ * log.cpp
+ *
+ *  Created on: Nov 11, 2009
+ *      Author: Adam Auton
+ *      ($Revision: 66 $)
+ */
+
+#include "output_log.h"
+
+void printLOG(string s)
+{
+	LOG << s; LOG.flush();
+	cout << s; cout.flush();
+}
+
+void error(string err_msg, int error_code)
+{
+	printLOG("Error:" + err_msg + "\n");
+	exit(error_code);
+}
+
+
+void error(string err_msg, double value1, double value2, int error_code)
+{
+	printLOG("Error:" + err_msg + "\n");
+	stringstream ss;
+	ss << "Value1=" << value1 << " Value2=" << value2 << endl;
+	printLOG(ss.str());
+	exit(error_code);
+}
+
+void warning(string err_msg)
+{
+	printLOG(err_msg + "\n");
+}
+
+void one_off_warning(string err_msg)
+{
+	static set<string> previous_warnings;
+	if (previous_warnings.find(err_msg) == previous_warnings.end())
+	{
+		printLOG(err_msg + "\n");
+		previous_warnings.insert(err_msg);
+	}
+}
+
+string int2str(int n)
+{
+  std::ostringstream s2( std::stringstream::out );
+  s2 << n;
+  return s2.str();
+}
+
+string longint2str(long int n)
+{
+  std::ostringstream s2( std::stringstream::out );
+  s2 << n;
+  return s2.str();
+}
+
+string dbl2str(double n, int prc)
+{
+  std::ostringstream s2;
+  if ( prc > 0 )
+    s2.precision(prc);
+  s2 << n;
+  return s2.str();
+}
+
+string dbl2str_fixed(double n, int prc)
+{
+  std::ostringstream s2;
+  s2 << setiosflags( ios::fixed );
+  if ( prc > 0 )
+    s2.precision(prc);
+  s2 << n;
+  return s2.str();
+}

data/ext/vcftools/cpp/.svn/text-base/output_log.h.svn-base

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+/*
+ * log.h
+ *
+ *  Created on: Nov 11, 2009
+ *      Author: Adam Auton
+ *      ($Revision: 91 $)
+ */
+
+#ifndef LOG_H_
+#define LOG_H_
+
+#include <cstdio>
+#include <cstdlib>
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <set>
+#include <sstream>
+
+using namespace std;
+
+extern ofstream LOG;
+
+void printLOG(string s);
+void error(string err_msg, int error_code=0);
+void error(string err_msg, double value1, double value2, int error_code=0);
+void warning(string err_msg);
+void one_off_warning(string err_msg);
+string int2str(int n);
+string longint2str(long int n);
+string dbl2str(double n, int prc);
+string dbl2str_fixed(double n, int prc);
+
+#endif /* LOG_H_ */