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annotate clustalomega/clustal-omega-0.2.0/src/clustal/symmatrix.c @ 0:ff1768533a07

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Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author clustalomega
date Tue, 07 Jun 2011 17:04:25 -0400
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1 /* -*- mode: c; tab-width: 4; c-basic-offset: 4; indent-tabs-mode: nil -*- */
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2
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3 /*********************************************************************
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4 * Clustal Omega - Multiple sequence alignment
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5 *
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6 * Copyright (C) 2010 University College Dublin
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7 *
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8 * Clustal-Omega is free software; you can redistribute it and/or
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9 * modify it under the terms of the GNU General Public License as
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10 * published by the Free Software Foundation; either version 2 of the
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11 * License, or (at your option) any later version.
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12 *
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13 * This file is part of Clustal-Omega.
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14 *
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15 ********************************************************************/
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16
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17 /*
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18 * RCS $Id: symmatrix.c 230 2011-04-09 15:37:50Z andreas $
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19 *
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20 *
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21 * Functions for symmetric (square) matrices including diagonal.
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22 * supports the notion of non-square sub-matrices of a symmetric
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23 * matrix, i.e. where |rows|<|cols|.
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24 *
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25 * FIXME Allocating one big chunk of memory is probably
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26 * much faster and also easier to maintain.
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27 */
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28
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29 #ifdef HAVE_CONFIG_H
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30 #include "config.h"
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31 #endif
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32
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33 #include <stdlib.h>
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34 #include <stdio.h>
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35 #include <ctype.h>
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36 #include <string.h>
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37 #include <assert.h>
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38 #include "symmatrix.h"
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39
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40
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41 #if 0
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42 #define DEBUG
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43 #endif
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44
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45 #define MAX_BUF_SIZE 65536
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46
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47 /**
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48 * @brief Allocates symmat and its members and initialises them. Data
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49 * will be calloced, i.e. initialised with zeros.
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50 *
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51 * @param[out] symmat
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52 * newly allocated and initialised symmatrix instance
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53 * @param[in] nrows
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54 * number of rows
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55 * @param[in]
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56 * ncols number of columns
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57 *
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58 * @return: non-zero on error
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59 *
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60 * @see FreeSymMatrix()
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61 *
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62 * @note: symmat data will be of fake shape nrows x ncols
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63 *
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64 */
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65 int
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66 NewSymMatrix(symmatrix_t **symmat, int nrows, int ncols)
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67 {
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68 int i; /* aux */
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69
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70 assert(nrows>0 && ncols>0 && ncols>=nrows);
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71 assert(ncols>0 && ncols>=nrows);
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72
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73 (*symmat) = (symmatrix_t *) malloc(1*sizeof(symmatrix_t));
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74 if (NULL == (*symmat)) {
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75 fprintf(stderr, "Couldn't allocate memory (%s|%s)\n",
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76 __FILE__, __FUNCTION__);
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77 return -1;
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78 }
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79
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80 (*symmat)->data = (double **) malloc(nrows * sizeof(double *));
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81 if (NULL == (*symmat)->data) {
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82 fprintf(stderr, "Couldn't allocate memory (%s|%s)\n",
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83 __FILE__, __FUNCTION__);
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84 free(*symmat);
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85 *symmat = NULL;
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86 return -1;
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87 }
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88 for (i=0; i<nrows; i++) {
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89 (*symmat)->data[i] = (double *) calloc((ncols-i), sizeof(double));
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90 if (NULL == (*symmat)->data[i]) {
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91 fprintf(stderr, "Couldn't allocate memory (%s|%s)\n",
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92 __FILE__, __FUNCTION__);
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93 while (0!=--i) {
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94 free((*symmat)->data[i]);
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95 }
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96 free((*symmat)->data);
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97 free(*symmat);
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98 *symmat = NULL;
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99 return -1;
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100 }
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101 #ifdef TRACE
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102 fprintf(stderr, "DEBUG(%s|%s():%d) initialising symmat with the number of the beast\n",
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103 __FILE__, __FUNCTION__, __LINE__);
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104 {
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105 int j;
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106 for (j=0; j<ncols-i; j++) {
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107 (*symmat)->data[i][j] = -666.0;
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108 }
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109
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110 }
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111 #endif
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112 }
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113
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114 (*symmat)->nrows = nrows;
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115 (*symmat)->ncols = ncols;
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116
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117 return 0;
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118 }
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119 /*** end: new_symmatrix ***/
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120
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121
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122 /**
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123 * @brief Sets symmat data of given index to given value
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124 *
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125 * @param[in] symmat
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126 * symmatrix_t whose data is to be set
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127 * @param[in] i
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128 * first index
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129 * @param[in] j
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130 * second index
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131 * @param[in] value
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132 * value used to set data point
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133 *
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134 * @see SymMatrixGetValue()
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135 *
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136 * @note This is a convenience function that checks index order.
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137 *
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138 */
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139 void
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140 SymMatrixSetValue(symmatrix_t *symmat, const int i, const int j, const double value)
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141 {
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142 assert(NULL != symmat);
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143
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144 if (i<=j) {
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145 assert(i < symmat->nrows && j < symmat->ncols);
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146 symmat->data[i][j-i] = value;
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147 } else {
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148 assert(j < symmat->nrows && i < symmat->ncols);
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149 symmat->data[j][i-j] = value;
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150 }
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151 }
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152 /*** end: symmatrix_setvalue ***/
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153
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154
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155
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156 /**
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157 * @brief Returns element of symmat corresponding to given indices
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158 *
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159 * @param[in] symmat
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160 * symmatrix_t of question
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161 * @param[in] i
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162 * index i
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163 * @param[in] j
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164 * index j
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165 *
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166 * @return requested value
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167 *
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168 * @see SymMatrixSetValue()
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169 *
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170 * @note This is a convenience function that checks index order.
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171 */
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172 double
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173 SymMatrixGetValue(symmatrix_t *symmat, const int i, const int j)
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174 {
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175 assert(NULL != symmat);
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176
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177 if (i<=j) {
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178 assert(i < symmat->nrows && j < symmat->ncols);
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179 return symmat->data[i][j-i];
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180 } else {
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181 assert(j < symmat->nrows && i < symmat->ncols);
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182 return symmat->data[j][i-j];
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183 }
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184 }
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185 /*** end: symmatrix_getvalue ***/
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186
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187
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188
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189
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190
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191 /**
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192 * @brief Returns a pointer to an element of symmat corresponding to
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193 * given indices
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194 *
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195 * @param[out] val
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196 * Value to be set
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197 * @param[in] symmat
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198 * symmatrix_t of question
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199 * @param[in] i
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200 * index i
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201 * @param[in] j
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202 * index j
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203 *
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204 * @return pointer to value
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205 *
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206 * @see SymMatrixGetValue()
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207 *
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208 * @note This is a convenience function that checks index order.
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209 *
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210 */
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211 void
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212 SymMatrixGetValueP(double **val, symmatrix_t *symmat,
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213 const int i, const int j)
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214 {
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215 assert(NULL != symmat);
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216
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217 if (i<=j) {
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218 assert(i < symmat->nrows && j < symmat->ncols);
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219 *val = &(symmat->data[i][j-i]);
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220 } else {
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221 assert(j < symmat->nrows && i < symmat->ncols);
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222 *val = &(symmat->data[j][i-j]);
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223 }
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224 }
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225 /*** end: symmatrix_getvaluep ***/
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226
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227
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228 /**
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229 * @brief Frees memory allocated by data members of symmat and symmat
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230 * itself.
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231 *
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232 * @param[in] symmat
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233 * symmatrix_t to be freed
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234 *
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235 * @note Use in conjunction with NewSymMatrix()
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236 *
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237 * @see NewSymMatrix()
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238 *
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239 */
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240 void
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241 FreeSymMatrix(symmatrix_t **symmat)
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242 {
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243 int i;
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244 if (NULL != (*symmat)) {
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245 if (NULL != (*symmat)->data) {
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246 for (i=0; i<(*symmat)->nrows; i++) {
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247 free((*symmat)->data[i]);
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248 }
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249 free((*symmat)->data);
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250 }
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251 }
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252 free(*symmat);
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253 *symmat = NULL;
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254 }
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255 /*** end: free_symmatrix ***/
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256
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257
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258
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259 /**
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260 * @brief Print out a symmat in phylip style. Distances are printed on
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261 * one line per sequence/object. Since we also support matrices with
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262 * rows\<cols, the first line can also be nrows by ncolumns instead
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263 * of just nrows
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264 *
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265 * @param[in] symmat
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266 * the symmatrix_t to print
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267 * @param[in] labels
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268 * sequence/objects labels/names. must be at least of length symmat nrows
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269 * @param[in] path
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270 * filename or NULL. If NULL stdout will be used.
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271 *
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272 */
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273 void
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274 SymMatrixPrint(symmatrix_t *symmat, char **labels, const char *path)
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275 {
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276 FILE *fp = NULL;
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277 int i, j; /* aux */
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278 int max_label_len = 0;
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279
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280 if (NULL==symmat || NULL==labels) {
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281 fprintf(stderr,
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282 "One of the provided arguments is empty or NULL (print_matrix)\n");
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283 return;
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284 }
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285 if (NULL==path) {
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286 fp = stdout;
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287 } else {
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288 if (NULL==(fp=fopen(path, "w"))) {
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289 fprintf(stderr, "Couldn't open %s for writing.", path);
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290 return;
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291 }
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292 }
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293
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294 /* find maximum label length for pretty printing
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295 */
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296 for (i=0; i<symmat->nrows; i++) {
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297 int this_len;
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298 assert(NULL != labels[i]);
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299 this_len = strlen(labels[i]);
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300 if (this_len>max_label_len)
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301 max_label_len = this_len;
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302 }
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303
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304 if (symmat->ncols==symmat->nrows) {
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305 fprintf(fp, "%u\n", symmat->ncols);
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306 } else {
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307 /* this is not standard phylip, but necessary to indicate
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308 seed matrices */
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309 fprintf(fp, "%u x %u\n", symmat->nrows, symmat->ncols);
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310 }
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311 for (i=0; i<symmat->nrows; i++) {
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312 /* phylip restriction is 10 characters. we don't care here
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313 */
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314 fprintf(fp, "%-*s", max_label_len, labels[i]);
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315 /* we are lazy and do it like fastdist: write all distances
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316 * for one seq to one line
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317 */
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318 for (j=0; j<symmat->ncols; j++) {
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319 fprintf(fp, " %f", SymMatrixGetValue(symmat, i, j));
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320 }
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321 fprintf(fp, "%s", "\n");
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322 }
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323 if (NULL != path) {
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324 (void) fclose(fp);
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325 } else {
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parents:
diff changeset
326 (void) fflush(fp);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
327 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
328 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
329 /*** end: SymMatrixPrint ***/
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
330
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
331
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
332
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
333 /**
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
334 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
335 * @brief Read a distance matrix in phylip format
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
336 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
337 * @param[in] pcFileIn
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
338 * distance matrix filename
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
339 * @param[out] prSymMat_p
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
340 * the symmatrix_t. will be allocated here.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
341 * @return:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
342 * non-zero on error
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
343 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
344 * @note:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
345 * FIXME untested code
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
346 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
347 int
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
348 SymMatrixRead(char *pcFileIn, symmatrix_t **prSymMat_p)
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
349 {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
350 FILE *prFilePointer;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
351 char *buf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
352 /* number of parsed sequences */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
353 int iNParsedSeq = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
354 /* number of parsed distances per sequence */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
355 int iNParsedDists = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
356 /* total number of sequences/objects */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
357 int iTotalNSeq = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
358 int iRetCode = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
359
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
360 assert(NULL!=pcFileIn);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
361
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
362 /* FIXME: test correctness and implement label checking */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
363 fprintf(stderr, "WARNING: Reading of distance matrix from file not thoroughly tested!\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
364 fprintf(stderr, "WARNING: Assuming same order of sequences in sequence file and distance matrix file (matching of labels not implemented)\n");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
365
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
366 if (NULL == (buf = (char *) malloc(MAX_BUF_SIZE * sizeof(char)))) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
367 fprintf(stderr, "ERROR: couldn't allocate memory at %s:%s:%d\n",
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
368 __FILE__, __FUNCTION__, __LINE__);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
369 return -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
370 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
371
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
372 if (NULL == (prFilePointer = fopen(pcFileIn, "r"))) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
373 fprintf(stderr, "ERROR: Couldn't open %s for reading\n", pcFileIn);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
374 free(buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
375 return -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
376 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
377
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
378 /* get number of sequences from first line and allocate memory for
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
379 * distance matrix
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
380 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
381 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
382 if (NULL == fgets(buf, MAX_BUF_SIZE, prFilePointer) ) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
383 fprintf(stderr, "Couldn't read first line from %s\n", pcFileIn);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
384 iRetCode = -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
385 goto closefile_and_freebuf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
386 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
387 if (strlen(buf)==MAX_BUF_SIZE-1) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
388 fprintf(stderr, "%s\n", "Looks like I couldn't read complete line. Wrong format (or too small MAX_BUF_SIZE)");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
389 iRetCode = -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
390 goto closefile_and_freebuf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
391 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
392 if (sscanf(buf, "%d", &iTotalNSeq)!=1) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
393 fprintf(stderr, "ERROR: couldn't parse number of sequences from first line of %s\n", pcFileIn);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
394 iRetCode = -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
395 goto closefile_and_freebuf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
396 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
397
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
398 #if TRACE
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
399 Log(&rLog, LOG_FORCED_DEBUG, "iTotalNSeq parsed from %s is %d\n", pcFileIn, iTotalNSeq);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
400 #endif
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
401
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
402 if (NewSymMatrix(prSymMat_p, iTotalNSeq, iTotalNSeq)) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
403 fprintf(stderr, "FATAL %s", "Memory allocation for distance matrix failed");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
404 iRetCode = -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
405 goto closefile_and_freebuf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
406 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
407
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
408
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
409 /* parse file line by line
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
410 *
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
411 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
412 while (NULL != fgets(buf, MAX_BUF_SIZE, prFilePointer)) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
413 char *szToken;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
414 int is_newseq;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
415
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
416 if (MAX_BUF_SIZE-1 == strlen(buf)) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
417 fprintf(stderr, "%s\n", "Looks like I couldn't read complete line. Wrong format (or too small MAX_BUF_SIZE)");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
418 iRetCode = -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
419 goto closefile_and_freebuf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
420 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
421
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
422 #ifdef DEBUG
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
423 Log(&rLog, LOG_FORCED_DEBUG, "Got line: %s\n", buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
424 #endif
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
425
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
426 /* new sequence label at beginning of line?
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
427 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
428 if (isblank(buf[0])) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
429 is_newseq = 0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
430 } else {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
431 is_newseq = 1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
432 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
433
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
434 /* tokenise line and treat new sequence specially
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
435 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
436 szToken = strtok(buf, " \t");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
437 if (is_newseq==1) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
438 iNParsedSeq++;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
439 iNParsedDists=0;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
440
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
441 /* if format is lower dimensional matrix then first
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
442 * sequence has no distances but might have newline
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
443 * character at it's end.
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
444 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
445 while (isspace(szToken[strlen(szToken)-1])) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
446 szToken[strlen(szToken)-1]='\0';
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
447 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
448 /* FIXME save label? */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
449 szToken = strtok(NULL, " \t");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
450 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
451 /* from here on it's only parsing of distances */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
452 while (szToken != NULL) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
453 double dist;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
454 iNParsedDists++;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
455
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
456 /* only parse what's needed */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
457 if (iNParsedDists!=iNParsedSeq) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
458 /* parse and store distance
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
459 */
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
460 if (sscanf(szToken, "%lf", &dist)!=1) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
461 fprintf(stderr, "Couldn't parse float from entry '%s'\n", szToken);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
462 iRetCode = -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
463 goto closefile_and_freebuf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
464 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
465 #if TRACE
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
466 Log(&rLog, LOG_FORCED_DEBUG, "Parsed distance %d for seq %d = %f\n", iNParsedDists-1, iNParsedSeq-1, dist);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
467 #endif
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
468 SymMatrixSetValue(*prSymMat_p, iNParsedSeq-1, iNParsedDists-1, dist);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
469 SymMatrixSetValue(*prSymMat_p, iNParsedDists-1, iNParsedSeq-1, dist);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
470 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
471 szToken = strtok(NULL, " \t");
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
472 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
473 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
474
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
475 if (iTotalNSeq!=iNParsedSeq) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
476 fprintf(stderr, "expected %d seqs, but only parsed %d\n", iTotalNSeq, iNParsedSeq);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
477 iRetCode = -1;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
478 goto closefile_and_freebuf;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
479 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
480 #if TRACE
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
481 for (i=0; i<iNParsedSeq; i++) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
482 int j;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
483 for (j=0; j<iNParsedSeq; j++) {
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff changeset
484 Log(&rLog, LOG_FORCED_DEBUG, "prSymMat_p[%d][%d]=%f\n", i, j, (*prSymMat_p)[i][j]);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
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485 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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486 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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487 #endif
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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488
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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489 closefile_and_freebuf:
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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490 fclose(prFilePointer);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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491 free(buf);
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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492
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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493 return iRetCode;
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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494 }
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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495 /*** end: SymMatrixRead ***/
ff1768533a07 Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
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496