1 | // ---------------------------------------------------------------------------- |
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2 | // probe_collection.cxx |
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3 | // ---------------------------------------------------------------------------- |
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4 | // Implementations of classes used to create and manage probe collections in Arb. |
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5 | // ---------------------------------------------------------------------------- |
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6 | |
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7 | |
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8 | #include "probe_collection.hxx" |
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9 | #include <xercesc/dom/DOM.hpp> |
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10 | #include <xercesc/dom/DOMDocument.hpp> |
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11 | #include <xercesc/dom/DOMDocumentType.hpp> |
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12 | #include <xercesc/dom/DOMElement.hpp> |
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13 | #include <xercesc/dom/DOMImplementation.hpp> |
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14 | #include <xercesc/dom/DOMImplementationLS.hpp> |
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15 | #include <xercesc/dom/DOMNodeIterator.hpp> |
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16 | #include <xercesc/dom/DOMNodeList.hpp> |
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17 | #include <xercesc/dom/DOMText.hpp> |
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18 | #include <xercesc/parsers/XercesDOMParser.hpp> |
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19 | #include <xercesc/util/XMLUni.hpp> |
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20 | #include <math.h> |
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21 | #include <arbdbt.h> |
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22 | #include <algorithm> |
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23 | |
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24 | using namespace xercesc; |
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25 | |
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26 | const size_t ArbMIN_PROBE_LENGTH = 6; |
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27 | |
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28 | typedef std::pair<const std::string, ArbMatchResult*> ArbMatchResultPtrStringPair; |
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29 | typedef std::pair<const double, ArbMatchResult*> ArbMatchResultPtrDoublePair; |
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30 | |
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31 | // ---------------------------------------------------------------------------- |
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32 | // Provide access to global objects |
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33 | // ---------------------------------------------------------------------------- |
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34 | |
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35 | ArbProbeCollection& get_probe_collection() { |
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36 | static ArbProbeCollection g_probe_collection; |
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37 | return g_probe_collection; |
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38 | } |
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39 | ArbMatchResultsManager& get_results_manager() { |
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40 | static ArbMatchResultsManager g_results_manager; |
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41 | return g_results_manager; |
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42 | } |
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43 | |
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44 | static ArbStringCache& get_string_cache() { |
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45 | static ArbStringCache g_string_cache; |
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46 | return g_string_cache; |
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47 | } |
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48 | |
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49 | // ---------------------------------------------------------------------------- |
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50 | // ArbStringCache method implementations |
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51 | // ---------------------------------------------------------------------------- |
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52 | void ArbStringCache::open() { |
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53 | char *uniqueName = GB_unique_filename("ArbString", "cache"); |
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54 | char *pTmpFileName = GB_create_tempfile(uniqueName); |
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55 | |
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56 | if (pTmpFileName != 0) { |
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57 | WriteCacheFile = fopen(pTmpFileName, "wb"); |
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58 | ReadCacheFile = fopen(pTmpFileName, "rb"); |
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59 | IsOpen = ((WriteCacheFile != 0) && (ReadCacheFile != 0)); |
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60 | FileName = pTmpFileName; |
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61 | } |
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62 | |
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63 | free(pTmpFileName); |
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64 | free(uniqueName); |
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65 | } |
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66 | |
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67 | // ---------------------------------------------------------------------------- |
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68 | |
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69 | void ArbStringCache::close() { |
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70 | if (ReadCacheFile != 0) { |
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71 | fclose(ReadCacheFile); |
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72 | |
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73 | ReadCacheFile = 0; |
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74 | } |
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75 | |
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76 | if (WriteCacheFile != 0) { |
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77 | fclose(WriteCacheFile); |
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78 | unlink(FileName.c_str()); |
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79 | |
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80 | WriteCacheFile = 0; |
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81 | } |
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82 | |
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83 | if (ReadBuffer != 0) { |
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84 | delete [] ReadBuffer; |
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85 | ReadBuffer = 0; |
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86 | } |
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87 | |
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88 | ReadBufferLength = 0; |
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89 | IsOpen = false; |
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90 | } |
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91 | |
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92 | // ---------------------------------------------------------------------------- |
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93 | |
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94 | bool ArbStringCache::allocReadBuffer(int nLength) const { |
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95 | if (nLength + 1 > ReadBufferLength) { |
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96 | if (ReadBuffer != 0) { |
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97 | delete [] ReadBuffer; |
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98 | } |
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99 | |
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100 | ReadBufferLength = nLength + 1; |
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101 | ReadBuffer = new char[ReadBufferLength]; |
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102 | } |
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103 | |
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104 | return (ReadBuffer != 0); |
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105 | } |
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106 | |
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107 | // ---------------------------------------------------------------------------- |
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108 | |
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109 | ArbStringCache::ArbStringCache() { |
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110 | IsOpen = false; |
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111 | WriteCacheFile = 0; |
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112 | ReadCacheFile = 0; |
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113 | ReadBuffer = 0; |
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114 | ReadBufferLength = 0; |
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115 | |
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116 | open(); |
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117 | } |
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118 | |
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119 | // ---------------------------------------------------------------------------- |
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120 | |
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121 | ArbStringCache::~ArbStringCache() { |
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122 | close(); |
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123 | } |
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124 | |
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125 | // ---------------------------------------------------------------------------- |
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126 | |
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127 | bool ArbStringCache::saveString(const char *pString, ArbCachedString& rCachedString) { |
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128 | bool bSaved = saveString(pString, strlen(pString), rCachedString); |
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129 | |
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130 | return (bSaved); |
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131 | } |
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132 | |
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133 | // ---------------------------------------------------------------------------- |
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134 | |
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135 | bool ArbStringCache::saveString(const char *pString, int nLength, ArbCachedString& rCachedString) { |
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136 | bool bSaved = false; |
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137 | |
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138 | if (IsOpen && (pString != 0)) { |
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139 | rCachedString.Len = nLength; |
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140 | |
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141 | fgetpos(WriteCacheFile, &rCachedString.Pos); |
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142 | fwrite(pString, nLength * sizeof(char), 1, WriteCacheFile); |
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143 | |
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144 | bSaved = true; |
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145 | } |
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146 | |
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147 | return (bSaved); |
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148 | } |
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149 | |
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150 | // ---------------------------------------------------------------------------- |
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151 | |
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152 | bool ArbStringCache::loadString(std::string& rString, const ArbCachedString& rCachedString) const { |
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153 | bool bLoaded = false; |
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154 | |
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155 | if (IsOpen && |
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156 | (rCachedString.Len > 0) && |
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157 | allocReadBuffer(rCachedString.Len)) |
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158 | { |
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159 | fpos_t nPos = rCachedString.Pos; |
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160 | fsetpos(ReadCacheFile, &nPos); |
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161 | |
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162 | size_t read = fread(ReadBuffer, sizeof(char), rCachedString.Len, ReadCacheFile); |
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163 | if (read == size_t(rCachedString.Len)) { |
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164 | ReadBuffer[rCachedString.Len] = '\0'; |
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165 | |
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166 | rString = ReadBuffer; |
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167 | bLoaded = true; |
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168 | } |
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169 | } |
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170 | |
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171 | return (bLoaded); |
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172 | } |
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173 | |
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174 | // ---------------------------------------------------------------------------- |
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175 | |
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176 | void ArbStringCache::flush() { |
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177 | if (IsOpen) { |
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178 | // Close and re-open to delete old cache file and create a new one |
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179 | close(); |
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180 | open(); |
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181 | } |
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182 | } |
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183 | |
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184 | |
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185 | // ---------------------------------------------------------------------------- |
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186 | // ArbProbeMatchWeighting method implementations |
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187 | // ---------------------------------------------------------------------------- |
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188 | int ArbProbeMatchWeighting::toIndex(char nC) const { |
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189 | int nIndex = 0; |
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190 | |
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191 | switch (nC) { |
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192 | case 'A': |
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193 | case 'a': { |
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194 | nIndex = 0; |
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195 | break; |
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196 | } |
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197 | |
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198 | case 'C': |
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199 | case 'c': { |
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200 | nIndex = 1; |
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201 | break; |
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202 | } |
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203 | |
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204 | case 'G': |
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205 | case 'g': { |
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206 | nIndex = 2; |
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207 | break; |
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208 | } |
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209 | |
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210 | case 'U': |
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211 | case 'u': |
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212 | case 'T': |
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213 | case 't': { |
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214 | nIndex = 3; |
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215 | break; |
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216 | } |
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217 | |
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218 | default: { |
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219 | arb_assert(0); |
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220 | break; |
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221 | } |
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222 | } |
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223 | |
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224 | return (nIndex); |
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225 | } |
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226 | |
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227 | // ---------------------------------------------------------------------------- |
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228 | |
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229 | double ArbProbeMatchWeighting::positionalWeight(int nPos, int nLength) const { |
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230 | double dS = -(::log(10) / Width); |
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231 | double dP = ((2.0 * nPos - nLength) / nLength) - Bias; |
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232 | double dWeight = ::exp(dS * dP * dP); |
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233 | |
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234 | return (dWeight); |
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235 | } |
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236 | |
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237 | // ---------------------------------------------------------------------------- |
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238 | |
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239 | void ArbProbeMatchWeighting::copy(const ArbProbeMatchWeighting& rCopy) { |
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240 | Width = rCopy.Width; |
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241 | Bias = rCopy.Bias; |
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242 | |
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243 | for (int cx = 0 ; cx < 4 ; cx++) { |
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244 | for (int cy = 0 ; cy < 4 ; cy++) { |
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245 | PenaltyMatrix[cy][cx] = rCopy.PenaltyMatrix[cy][cx]; |
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246 | } |
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247 | } |
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248 | } |
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249 | |
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250 | // ---------------------------------------------------------------------------- |
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251 | |
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252 | ArbProbeMatchWeighting::ArbProbeMatchWeighting() |
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253 | : ArbRefCount(), |
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254 | PenaltyMatrix() |
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255 | { |
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256 | float aDefaultValues[16] = { |
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257 | 0.0, 1.0, 1.0, 1.0, |
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258 | 1.0, 0.0, 1.0, 1.0, |
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259 | 1.0, 1.0, 0.0, 1.0, |
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260 | 1.0, 1.0, 1.0, 0.0 |
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261 | }; |
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262 | |
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263 | float dWidth = 1.0; |
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264 | float dBias = 0.0; |
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265 | |
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266 | initialise(aDefaultValues, dWidth, dBias); |
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267 | } |
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268 | |
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269 | // ---------------------------------------------------------------------------- |
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270 | |
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271 | ArbProbeMatchWeighting::ArbProbeMatchWeighting(const float aValues[16], float dWidth, float dBias) |
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272 | : ArbRefCount(), |
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273 | PenaltyMatrix() |
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274 | { |
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275 | Width = 1.0; |
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276 | Bias = 0.0; |
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277 | |
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278 | initialise(aValues, dWidth, dBias); |
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279 | } |
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280 | |
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281 | // ---------------------------------------------------------------------------- |
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282 | |
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283 | ArbProbeMatchWeighting::ArbProbeMatchWeighting(const ArbProbeMatchWeighting& rCopy) |
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284 | : ArbRefCount(), |
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285 | PenaltyMatrix() |
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286 | { |
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287 | copy(rCopy); |
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288 | } |
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289 | |
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290 | // ---------------------------------------------------------------------------- |
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291 | |
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292 | ArbProbeMatchWeighting::~ArbProbeMatchWeighting() { |
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293 | // Do Nothing |
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294 | } |
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295 | |
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296 | // ---------------------------------------------------------------------------- |
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297 | |
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298 | ArbProbeMatchWeighting& ArbProbeMatchWeighting::operator = (const ArbProbeMatchWeighting& rCopy) { |
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299 | copy(rCopy); |
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300 | return *this; |
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301 | } |
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302 | |
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303 | // ---------------------------------------------------------------------------- |
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304 | |
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305 | void ArbProbeMatchWeighting::initialise(const float aValues[16], float dWidth, float dBias) { |
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306 | Width = dWidth; |
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307 | Bias = dBias; |
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308 | |
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309 | int cz = 0; |
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310 | |
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311 | for (int cx = 0 ; cx < 4 ; cx++) { |
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312 | for (int cy = 0 ; cy < 4 ; cy++) { |
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313 | PenaltyMatrix[cy][cx] = aValues[cz]; |
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314 | |
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315 | cz++; |
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316 | } |
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317 | } |
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318 | } |
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319 | |
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320 | // ---------------------------------------------------------------------------- |
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321 | |
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322 | bool ArbProbeMatchWeighting::initialise(const char *pCSValues, const char *pCSWidth, const char *pCSBias) { |
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323 | bool bInitialised = false; |
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324 | |
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325 | if ((pCSValues != 0) && |
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326 | (pCSWidth != 0) && |
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327 | (pCSBias != 0)) |
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328 | { |
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329 | float dWidth = 0; |
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330 | float dBias = 0; |
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331 | float aValues[16] = { |
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332 | 0.0, 1.0, 1.0, 1.0, |
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333 | 1.0, 0.0, 1.0, 1.0, |
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334 | 1.0, 1.0, 0.0, 1.0, |
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335 | 1.0, 1.0, 1.0, 0.0 |
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336 | }; |
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337 | |
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338 | int nItems = ::sscanf(pCSValues, |
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339 | "%f%f%f%f" |
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340 | "%f%f%f%f" |
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341 | "%f%f%f%f" |
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342 | "%f%f%f%f", |
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343 | aValues, aValues + 1, aValues + 2, aValues + 3, |
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344 | aValues + 4, aValues + 5, aValues + 6, aValues + 7, |
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345 | aValues + 8, aValues + 9, aValues + 10, aValues + 11, |
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346 | aValues + 12, aValues + 13, aValues + 14, aValues + 15); |
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347 | |
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348 | nItems += ::sscanf(pCSWidth, "%f", &dWidth); |
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349 | nItems += ::sscanf(pCSBias, "%f", &dBias); |
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350 | |
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351 | if (nItems == (16 + 2)) { |
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352 | initialise(aValues, dWidth, dBias); |
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353 | |
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354 | bInitialised = true; |
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355 | } |
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356 | } |
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357 | |
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358 | return (bInitialised); |
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359 | } |
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360 | |
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361 | // ---------------------------------------------------------------------------- |
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362 | |
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363 | void ArbProbeMatchWeighting::getParameters(float aValues[16], float& dWidth, float& dBias) const { |
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364 | int cz = 0; |
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365 | |
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366 | for (int cx = 0 ; cx < 4 ; cx++) { |
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367 | for (int cy = 0 ; cy < 4 ; cy++) { |
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368 | aValues[cz] = PenaltyMatrix[cy][cx]; |
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369 | |
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370 | cz++; |
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371 | } |
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372 | } |
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373 | |
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374 | dWidth = Width; |
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375 | dBias = Bias; |
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376 | } |
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377 | |
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378 | // ---------------------------------------------------------------------------- |
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379 | |
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380 | void ArbProbeMatchWeighting::writeXML(FILE *hFile, const char *pPrefix) const { |
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381 | bool bFirst = true; |
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382 | |
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383 | ::fprintf(hFile, "%s<match_weighting width=\"%g\" bias=\"%g\">\n", pPrefix, Width, Bias); |
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384 | ::fprintf(hFile, "%s <penalty_matrix values=\"", pPrefix); |
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385 | |
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386 | for (int cx = 0 ; cx < 4 ; cx++) { |
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387 | for (int cy = 0 ; cy < 4 ; cy++) { |
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388 | if (bFirst) { |
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389 | ::fprintf(hFile, "%g", PenaltyMatrix[cy][cx]); |
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390 | |
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391 | bFirst = false; |
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392 | } |
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393 | else { |
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394 | ::fprintf(hFile, " %g", PenaltyMatrix[cy][cx]); |
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395 | } |
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396 | } |
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397 | } |
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398 | |
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399 | ::fprintf(hFile, "\"/>\n"); |
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400 | ::fprintf(hFile, "%s</match_weighting>\n", pPrefix); |
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401 | } |
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402 | |
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403 | // ---------------------------------------------------------------------------- |
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404 | |
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405 | double ArbProbeMatchWeighting::matchWeight(const char *pSequenceA, const char *pSequenceB) const { |
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406 | double dWeight = -1.0; |
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407 | |
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408 | if ((pSequenceA != 0) && (pSequenceB != 0)) { |
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409 | int nLengthA = strlen(pSequenceA); |
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410 | int nLengthB = strlen(pSequenceB); |
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411 | int nLength = (nLengthA < nLengthB) ? nLengthA : nLengthB; |
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412 | |
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413 | const char *pA = pSequenceA; |
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414 | const char *pB = pSequenceB; |
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415 | |
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416 | dWeight = 0.0; |
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417 | |
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418 | for (int cn = 0 ; cn < nLength ; cn++) { |
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419 | switch (*pA) { |
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420 | case 'N': |
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421 | case 'n': { |
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422 | // Wildcard match so don't penalise it |
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423 | break; |
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424 | } |
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425 | |
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426 | default: { |
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427 | switch (*pB) { |
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428 | case 'N': |
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429 | case 'n': { |
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430 | // Wildcard match so don't penalise it |
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431 | break; |
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432 | } |
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433 | |
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434 | default: { |
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435 | dWeight += PenaltyMatrix[toIndex(*pA)][toIndex(*pB)] * positionalWeight(cn, nLength); |
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436 | break; |
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437 | } |
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438 | } |
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439 | break; |
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440 | } |
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441 | } |
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442 | |
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443 | pA++; |
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444 | pB++; |
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445 | } |
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446 | } |
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447 | else { |
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448 | arb_assert(0); |
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449 | } |
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450 | |
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451 | return (dWeight); |
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452 | } |
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453 | |
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454 | // ---------------------------------------------------------------------------- |
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455 | |
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456 | double ArbProbeMatchWeighting::matchWeightResult(const char *pProbeSequence, const char *pMatchResult) const { |
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457 | double dWeight = -1.0; |
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458 | |
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459 | if ((pProbeSequence != 0) && (pMatchResult != 0)) { |
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460 | int nMatchLength; |
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461 | int nLengthResult = strlen(pMatchResult); |
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462 | int nLength = strlen(pProbeSequence); |
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463 | |
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464 | const char *pS = pProbeSequence; |
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465 | const char *pR = pMatchResult; |
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466 | int cn; |
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467 | |
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468 | if (nLength <= nLengthResult) { |
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469 | nMatchLength = nLength; |
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470 | } |
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471 | else { |
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472 | nMatchLength = nLengthResult; |
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473 | } |
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474 | |
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475 | dWeight = 0.0; |
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476 | |
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477 | for (cn = 0 ; cn < nMatchLength ; cn++) { |
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478 | char cB; |
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479 | |
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480 | switch (*pR) { |
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481 | case '-': |
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482 | case '=': { |
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483 | cB = *pS; |
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484 | break; |
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485 | } |
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486 | |
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487 | // I have no idea about this one. There is no mention in Arb about what |
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488 | // .... means in terms of match results so I'll just assume it to be the |
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489 | // same as U |
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490 | case '.': { |
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491 | cB = 'U'; |
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492 | break; |
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493 | } |
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494 | |
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495 | default: { |
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496 | cB = *pR; |
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497 | break; |
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498 | } |
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499 | } |
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500 | |
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501 | switch (*pS) { |
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502 | case 'N': |
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503 | case 'n': { |
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504 | // Wildcard match so don't penalise it |
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505 | break; |
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506 | } |
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507 | |
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508 | default: { |
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509 | switch (cB) { |
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510 | case 'N': |
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511 | case 'n': { |
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512 | // Wildcard match so don't penalise it |
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513 | break; |
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514 | } |
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515 | |
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516 | default: { |
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517 | dWeight += PenaltyMatrix[toIndex(*pS)][toIndex(cB)] * positionalWeight(cn, nLength); |
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518 | break; |
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519 | } |
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520 | } |
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521 | break; |
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522 | } |
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523 | } |
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524 | |
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525 | pS++; |
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526 | pR++; |
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527 | } |
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528 | |
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529 | int nNoMatch = toIndex('U'); |
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530 | |
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531 | for (; cn < nLength ; cn++) { |
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532 | dWeight += PenaltyMatrix[toIndex(*pS)][nNoMatch] * positionalWeight(cn, nLength); |
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533 | |
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534 | pS++; |
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535 | } |
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536 | } |
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537 | else { |
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538 | arb_assert(0); |
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539 | } |
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540 | |
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541 | return (dWeight); |
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542 | } |
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543 | |
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544 | |
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545 | // ---------------------------------------------------------------------------- |
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546 | // ArbProbe method implementations |
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547 | // ---------------------------------------------------------------------------- |
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548 | ArbProbe::ArbProbe() |
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549 | : ArbRefCount(), |
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550 | Name(), |
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551 | Sequence(), |
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552 | DisplayName() |
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553 | { |
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554 | // Do nothing |
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555 | } |
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556 | |
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557 | // ---------------------------------------------------------------------------- |
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558 | |
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559 | ArbProbe::ArbProbe(const char *pName, const char *pSequence) |
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560 | : ArbRefCount(), |
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561 | Name(), |
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562 | Sequence(), |
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563 | DisplayName() |
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564 | { |
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565 | nameAndSequence(pName, pSequence); |
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566 | } |
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567 | |
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568 | // ---------------------------------------------------------------------------- |
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569 | |
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570 | ArbProbe::ArbProbe(const ArbProbe& rCopy) |
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571 | : ArbRefCount(), |
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572 | Name(), |
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573 | Sequence(), |
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574 | DisplayName() |
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575 | { |
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576 | // Note that we do a copy of Name and Sequence via c_str() because std:string |
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577 | // shares internal buffers between strings if using a copy constructor and |
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578 | // this can potentially result in memory corrupting if the owner string is deleted |
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579 | // (REFCOUNT_HACK) |
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580 | nameAndSequence(rCopy.Name.c_str(), rCopy.Sequence.c_str()); |
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581 | } |
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582 | |
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583 | // ---------------------------------------------------------------------------- |
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584 | |
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585 | ArbProbe::~ArbProbe() { |
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586 | // Do nothing |
---|
587 | } |
---|
588 | |
---|
589 | // ---------------------------------------------------------------------------- |
---|
590 | |
---|
591 | void ArbProbe::writeXML(FILE *hFile, const char *pPrefix) const { |
---|
592 | ::fprintf(hFile, "%s<probe seq=\"%s\" name=\"%s\"/>\n", pPrefix, Sequence.c_str(), Name.c_str()); |
---|
593 | } |
---|
594 | |
---|
595 | // ---------------------------------------------------------------------------- |
---|
596 | |
---|
597 | void ArbProbe::nameAndSequence(const char *pName, const char *pSequence) { // REFCOUNT_HACK |
---|
598 | if (pName != 0) { |
---|
599 | Name = pName; |
---|
600 | } |
---|
601 | else { |
---|
602 | Name = ""; |
---|
603 | } |
---|
604 | |
---|
605 | if (pSequence != 0) { |
---|
606 | Sequence = pSequence; |
---|
607 | } |
---|
608 | else { |
---|
609 | Sequence = ""; |
---|
610 | |
---|
611 | arb_assert(0); |
---|
612 | } |
---|
613 | |
---|
614 | DisplayName = Name + ":" + Sequence; |
---|
615 | } |
---|
616 | |
---|
617 | // ---------------------------------------------------------------------------- |
---|
618 | |
---|
619 | int ArbProbe::allowedMismatches() const { |
---|
620 | size_t nProbe_Length = Sequence.length(); |
---|
621 | size_t nAllowedMistaches = (nProbe_Length - ArbMIN_PROBE_LENGTH) / 2; |
---|
622 | |
---|
623 | // Arb probe server doesn't seem to like having more that 20 mis-matches. |
---|
624 | if (nAllowedMistaches > 20) { |
---|
625 | nAllowedMistaches = 20; |
---|
626 | } |
---|
627 | |
---|
628 | return (nAllowedMistaches); |
---|
629 | } |
---|
630 | |
---|
631 | |
---|
632 | // ---------------------------------------------------------------------------- |
---|
633 | // ArbProbeCollection method implementations |
---|
634 | // ---------------------------------------------------------------------------- |
---|
635 | void ArbProbeCollection::flush() { |
---|
636 | ArbProbePtrListIter Iter; |
---|
637 | |
---|
638 | for (Iter = ProbeList.begin() ; Iter != ProbeList.end() ; ++Iter) { |
---|
639 | ArbProbe *pProbe = *Iter; |
---|
640 | |
---|
641 | if (pProbe != 0) { |
---|
642 | pProbe->free(); |
---|
643 | } |
---|
644 | } |
---|
645 | |
---|
646 | ProbeList.clear(); |
---|
647 | } |
---|
648 | |
---|
649 | // ---------------------------------------------------------------------------- |
---|
650 | |
---|
651 | void ArbProbeCollection::copy(const ArbProbePtrList& rList) { |
---|
652 | ArbProbePtrListConstIter Iter; |
---|
653 | |
---|
654 | for (Iter = rList.begin() ; Iter != rList.end() ; ++Iter) { |
---|
655 | ArbProbe *pProbe = *Iter; |
---|
656 | |
---|
657 | if (pProbe != 0) { |
---|
658 | ProbeList.push_back(pProbe); |
---|
659 | pProbe->lock(); |
---|
660 | } |
---|
661 | } |
---|
662 | } |
---|
663 | |
---|
664 | // ---------------------------------------------------------------------------- |
---|
665 | |
---|
666 | ArbProbeCollection::ArbProbeCollection() |
---|
667 | : ArbRefCount(), |
---|
668 | Name(), |
---|
669 | ProbeList(), |
---|
670 | MatchWeighting() |
---|
671 | { |
---|
672 | HasChanged = false; |
---|
673 | } |
---|
674 | |
---|
675 | // ---------------------------------------------------------------------------- |
---|
676 | |
---|
677 | ArbProbeCollection::ArbProbeCollection(const char *pName) |
---|
678 | : ArbRefCount(), |
---|
679 | Name(), |
---|
680 | ProbeList(), |
---|
681 | MatchWeighting() |
---|
682 | { |
---|
683 | // Note that we do a copy of Name via c_str() because std:string shares |
---|
684 | // internal buffers between strings if using a copy constructor and this can |
---|
685 | // potentially result in memory corrupting if the owner string is deleted |
---|
686 | // (REFCOUNT_HACK) |
---|
687 | name(pName); |
---|
688 | |
---|
689 | HasChanged = false; |
---|
690 | } |
---|
691 | |
---|
692 | // ---------------------------------------------------------------------------- |
---|
693 | |
---|
694 | ArbProbeCollection::ArbProbeCollection(const ArbProbeCollection& rCopy) |
---|
695 | : ArbRefCount(), |
---|
696 | Name(), |
---|
697 | ProbeList(), |
---|
698 | MatchWeighting(rCopy.MatchWeighting) |
---|
699 | { |
---|
700 | name(rCopy.name().c_str()); |
---|
701 | copy(rCopy.ProbeList); |
---|
702 | |
---|
703 | HasChanged = false; |
---|
704 | } |
---|
705 | |
---|
706 | // ---------------------------------------------------------------------------- |
---|
707 | |
---|
708 | ArbProbeCollection::~ArbProbeCollection() { |
---|
709 | flush(); |
---|
710 | } |
---|
711 | |
---|
712 | // ---------------------------------------------------------------------------- |
---|
713 | |
---|
714 | ArbProbeCollection& ArbProbeCollection::operator = (const ArbProbeCollection& rCopy) { |
---|
715 | flush(); |
---|
716 | name(rCopy.name().c_str()); |
---|
717 | copy(rCopy.ProbeList); |
---|
718 | |
---|
719 | MatchWeighting = rCopy.MatchWeighting; |
---|
720 | HasChanged = false; |
---|
721 | |
---|
722 | return (*this); |
---|
723 | } |
---|
724 | |
---|
725 | // ---------------------------------------------------------------------------- |
---|
726 | |
---|
727 | static bool elementHasName(DOMElement *pElement, const char *pName) { |
---|
728 | bool bHasName = false; |
---|
729 | |
---|
730 | if (pName != 0) { |
---|
731 | XMLCh *pNameStr; |
---|
732 | |
---|
733 | pNameStr = XMLString::transcode(pName); |
---|
734 | bHasName = XMLString::equals(pElement->getTagName(), pNameStr); |
---|
735 | XMLString::release(&pNameStr); |
---|
736 | } |
---|
737 | |
---|
738 | return (bHasName); |
---|
739 | } |
---|
740 | |
---|
741 | // ---------------------------------------------------------------------------- |
---|
742 | |
---|
743 | static bool isElement(DOMNode *pNode, DOMElement*& pElement, const char *pName) { |
---|
744 | bool bIsElement = false; |
---|
745 | |
---|
746 | if (pNode != 0) { |
---|
747 | short nNodeType = pNode->getNodeType(); |
---|
748 | |
---|
749 | if (nNodeType == DOMNode::ELEMENT_NODE) { |
---|
750 | pElement = dynamic_cast<xercesc::DOMElement*>(pNode); |
---|
751 | |
---|
752 | if (pName != 0) { |
---|
753 | bIsElement = elementHasName(pElement, pName); |
---|
754 | } |
---|
755 | else { |
---|
756 | bIsElement = true; |
---|
757 | } |
---|
758 | } |
---|
759 | } |
---|
760 | |
---|
761 | return (bIsElement); |
---|
762 | } |
---|
763 | |
---|
764 | // ---------------------------------------------------------------------------- |
---|
765 | |
---|
766 | bool ArbProbeCollection::openXML(const char *pFileAndPath, std::string& rErrorMessage) { |
---|
767 | bool bOpened = false; |
---|
768 | |
---|
769 | rErrorMessage = ""; |
---|
770 | |
---|
771 | if (pFileAndPath != 0 && pFileAndPath[0]) { |
---|
772 | struct stat FileStatus; |
---|
773 | int nResult = ::stat(pFileAndPath, &FileStatus); |
---|
774 | |
---|
775 | if ((nResult == 0) && !S_ISDIR(FileStatus.st_mode)) { |
---|
776 | flush(); |
---|
777 | |
---|
778 | XMLPlatformUtils::Initialize(); |
---|
779 | |
---|
780 | // We need braces to ensure Parser goes out of scope be Terminate() is called |
---|
781 | { |
---|
782 | XercesDOMParser Parser; |
---|
783 | |
---|
784 | Parser.setValidationScheme(XercesDOMParser::Val_Never); |
---|
785 | Parser.setDoNamespaces(false); |
---|
786 | Parser.setDoSchema(false); |
---|
787 | Parser.setLoadExternalDTD(false); |
---|
788 | |
---|
789 | try { |
---|
790 | Parser.parse(pFileAndPath); |
---|
791 | |
---|
792 | DOMDocument *pDoc = Parser.getDocument(); |
---|
793 | DOMElement *pRoot = pDoc->getDocumentElement(); |
---|
794 | |
---|
795 | if ((pRoot != 0) && elementHasName(pRoot, "probe_collection")) { |
---|
796 | char *pNameAttr = 0; |
---|
797 | XMLCh *pNameAttrStr = XMLString::transcode("name"); |
---|
798 | DOMNodeList *pPC_Children; |
---|
799 | XMLSize_t nPC_Count; |
---|
800 | bool bHasProbeList = false; |
---|
801 | bool bHasMatchWeighting = false; |
---|
802 | |
---|
803 | pNameAttr = XMLString::transcode(pRoot->getAttribute(pNameAttrStr)); |
---|
804 | name(pNameAttr); |
---|
805 | XMLString::release(&pNameAttr); |
---|
806 | |
---|
807 | pPC_Children = pRoot->getChildNodes(); |
---|
808 | nPC_Count = pPC_Children->getLength(); |
---|
809 | |
---|
810 | for (XMLSize_t cx = 0 ; cx < nPC_Count ; ++cx) { |
---|
811 | DOMNode *pPC_Node = pPC_Children->item(cx); |
---|
812 | DOMElement *pPC_Element = 0; |
---|
813 | |
---|
814 | if (isElement(pPC_Node, pPC_Element, "probe_list")) { |
---|
815 | DOMNodeList *pPL_Children; |
---|
816 | XMLSize_t nPL_Count; |
---|
817 | XMLCh *pSeqAttrStr; |
---|
818 | |
---|
819 | pSeqAttrStr = XMLString::transcode("seq"); |
---|
820 | pPL_Children = pPC_Element->getChildNodes(); |
---|
821 | nPL_Count = pPL_Children->getLength(); |
---|
822 | |
---|
823 | for (XMLSize_t cy = 0 ; cy < nPL_Count ; ++cy) { |
---|
824 | DOMNode *pPL_Node = pPL_Children->item(cy); |
---|
825 | DOMElement *pPL_Element = 0; |
---|
826 | char *pSeqAttr = 0; |
---|
827 | |
---|
828 | if (isElement(pPL_Node, pPL_Element, "probe")) { |
---|
829 | pNameAttr = XMLString::transcode(pPL_Element->getAttribute(pNameAttrStr)); |
---|
830 | pSeqAttr = XMLString::transcode(pPL_Element->getAttribute(pSeqAttrStr)); |
---|
831 | |
---|
832 | add(pNameAttr, pSeqAttr); |
---|
833 | |
---|
834 | XMLString::release(&pNameAttr); |
---|
835 | XMLString::release(&pSeqAttr); |
---|
836 | |
---|
837 | bHasProbeList = true; |
---|
838 | } |
---|
839 | } |
---|
840 | } |
---|
841 | else if (isElement(pPC_Node, pPC_Element, "match_weighting")) { |
---|
842 | DOMNodeList *pMW_Children; |
---|
843 | XMLSize_t nMW_Count; |
---|
844 | XMLCh *pWidthAttrStr = XMLString::transcode("width"); |
---|
845 | XMLCh *pBiasAttrStr = XMLString::transcode("bias"); |
---|
846 | char *pWidthStr = XMLString::transcode(pPC_Element->getAttribute(pWidthAttrStr)); |
---|
847 | char *pBiasStr = XMLString::transcode(pPC_Element->getAttribute(pBiasAttrStr)); |
---|
848 | |
---|
849 | pMW_Children = pPC_Element->getChildNodes(); |
---|
850 | nMW_Count = pMW_Children->getLength(); |
---|
851 | |
---|
852 | for (XMLSize_t cy = 0 ; cy < nMW_Count ; ++cy) { |
---|
853 | DOMNode *pPM_Node = pMW_Children->item(cy); |
---|
854 | DOMElement *pPM_Element = 0; |
---|
855 | |
---|
856 | if (isElement(pPM_Node, pPM_Element, "penalty_matrix")) { |
---|
857 | XMLCh *pValuesAttrStr = XMLString::transcode("values"); |
---|
858 | char *pValuesAttr = XMLString::transcode(pPM_Element->getAttribute(pValuesAttrStr)); |
---|
859 | |
---|
860 | if (MatchWeighting.initialise(pValuesAttr, pWidthStr, pBiasStr)) { |
---|
861 | bHasMatchWeighting = true; |
---|
862 | } |
---|
863 | else { |
---|
864 | rErrorMessage = "Too few penalty_matrix values"; |
---|
865 | } |
---|
866 | |
---|
867 | XMLString::release(&pValuesAttrStr); |
---|
868 | XMLString::release(&pValuesAttr); |
---|
869 | } |
---|
870 | } |
---|
871 | |
---|
872 | XMLString::release(&pWidthAttrStr); |
---|
873 | XMLString::release(&pBiasAttrStr); |
---|
874 | XMLString::release(&pWidthStr); |
---|
875 | XMLString::release(&pBiasStr); |
---|
876 | } |
---|
877 | } |
---|
878 | |
---|
879 | XMLString::release(&pNameAttrStr); |
---|
880 | |
---|
881 | bOpened = bHasProbeList && bHasMatchWeighting; |
---|
882 | |
---|
883 | if (!bHasProbeList) { |
---|
884 | rErrorMessage += "\nprobe_list missing or empty"; |
---|
885 | } |
---|
886 | |
---|
887 | if (!bHasMatchWeighting) { |
---|
888 | rErrorMessage += "\nmatch_weighting missing or empty"; |
---|
889 | } |
---|
890 | } |
---|
891 | |
---|
892 | if (bOpened) { |
---|
893 | HasChanged = false; |
---|
894 | } |
---|
895 | } |
---|
896 | catch (xercesc::DOMException& e1) { |
---|
897 | char *message = xercesc::XMLString::transcode(e1.getMessage()); |
---|
898 | |
---|
899 | rErrorMessage = "Error parsing file: "; |
---|
900 | rErrorMessage += message; |
---|
901 | |
---|
902 | XMLString::release(&message); |
---|
903 | } |
---|
904 | catch (xercesc::XMLException& e2) { |
---|
905 | char *message = xercesc::XMLString::transcode(e2.getMessage()); |
---|
906 | |
---|
907 | rErrorMessage = "Error parsing file: "; |
---|
908 | rErrorMessage += message; |
---|
909 | |
---|
910 | XMLString::release(&message); |
---|
911 | } |
---|
912 | } |
---|
913 | |
---|
914 | XMLPlatformUtils::Terminate(); |
---|
915 | } |
---|
916 | else if (nResult == EACCES) { |
---|
917 | rErrorMessage = "Search permission is denied"; |
---|
918 | } |
---|
919 | else if (nResult == EIO) { |
---|
920 | rErrorMessage = "Error reading from the file system"; |
---|
921 | } |
---|
922 | else if (nResult == ELOOP) { |
---|
923 | rErrorMessage = "Loop exists in symbolic links"; |
---|
924 | } |
---|
925 | else if (nResult == ENAMETOOLONG) { |
---|
926 | rErrorMessage = "Path name too long"; |
---|
927 | } |
---|
928 | else if (nResult == ENOENT) { |
---|
929 | rErrorMessage = "Component of path existing file or missing"; |
---|
930 | } |
---|
931 | else if (nResult == ENOTDIR) { |
---|
932 | rErrorMessage = "Component of path not a directory"; |
---|
933 | } |
---|
934 | else if (nResult == EOVERFLOW) { |
---|
935 | rErrorMessage = ""; |
---|
936 | } |
---|
937 | } |
---|
938 | else { |
---|
939 | rErrorMessage = "Please select a file to load"; |
---|
940 | } |
---|
941 | |
---|
942 | return (bOpened); |
---|
943 | } |
---|
944 | |
---|
945 | // ---------------------------------------------------------------------------- |
---|
946 | |
---|
947 | bool ArbProbeCollection::saveXML(const char *pFileAndPath) const { |
---|
948 | bool bSaved = false; |
---|
949 | |
---|
950 | if (pFileAndPath != 0) { |
---|
951 | FILE *hFile = ::fopen(pFileAndPath, "wt"); |
---|
952 | |
---|
953 | if (hFile != 0) { |
---|
954 | ArbProbePtrListConstIter Iter; |
---|
955 | |
---|
956 | ::fprintf(hFile, "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?>\n"); |
---|
957 | ::fprintf(hFile, "<!DOCTYPE probe_collection>\n"); |
---|
958 | ::fprintf(hFile, "<probe_collection name=\"%s\">\n", Name.c_str()); |
---|
959 | ::fprintf(hFile, " <probe_list>\n"); |
---|
960 | |
---|
961 | for (Iter = ProbeList.begin() ; Iter != ProbeList.end() ; ++Iter) { |
---|
962 | const ArbProbe *pProbe = *Iter; |
---|
963 | |
---|
964 | if (pProbe != 0) { |
---|
965 | pProbe->writeXML(hFile, " "); |
---|
966 | } |
---|
967 | } |
---|
968 | |
---|
969 | ::fprintf(hFile, " </probe_list>\n"); |
---|
970 | |
---|
971 | MatchWeighting.writeXML(hFile, " "); |
---|
972 | |
---|
973 | ::fprintf(hFile, "</probe_collection>\n"); |
---|
974 | |
---|
975 | ::fclose(hFile); |
---|
976 | |
---|
977 | HasChanged = false; |
---|
978 | } |
---|
979 | } |
---|
980 | |
---|
981 | return (bSaved); |
---|
982 | } |
---|
983 | |
---|
984 | // ---------------------------------------------------------------------------- |
---|
985 | |
---|
986 | void ArbProbeCollection::setParameters(const float aValues[16], float dWidth, float dBias) { |
---|
987 | MatchWeighting.setParameters(aValues, dWidth, dBias); |
---|
988 | |
---|
989 | HasChanged = true; |
---|
990 | } |
---|
991 | |
---|
992 | // ---------------------------------------------------------------------------- |
---|
993 | |
---|
994 | void ArbProbeCollection::getParameters(float aValues[16], float& dWidth, float& dBias) const { |
---|
995 | MatchWeighting.getParameters(aValues, dWidth, dBias); |
---|
996 | } |
---|
997 | |
---|
998 | // ---------------------------------------------------------------------------- |
---|
999 | |
---|
1000 | struct hasSequence { |
---|
1001 | std::string seq; |
---|
1002 | hasSequence(std::string seq_) : seq(seq_) {} |
---|
1003 | bool operator()(const ArbProbe *probe) { |
---|
1004 | return probe && probe->sequence() == seq; |
---|
1005 | } |
---|
1006 | }; |
---|
1007 | |
---|
1008 | const ArbProbe *ArbProbeCollection::find(const char *pSequence) const { |
---|
1009 | if (pSequence) { |
---|
1010 | ArbProbePtrListConstIter found = find_if(ProbeList.begin(), ProbeList.end(), hasSequence(pSequence)); |
---|
1011 | if (found != ProbeList.end()) { |
---|
1012 | return *found; |
---|
1013 | } |
---|
1014 | } |
---|
1015 | return NULL; |
---|
1016 | } |
---|
1017 | |
---|
1018 | // ---------------------------------------------------------------------------- |
---|
1019 | |
---|
1020 | bool ArbProbeCollection::add(const char *pName, const char *pSequence, const ArbProbe **ppProbe) { |
---|
1021 | bool bAdded = false; |
---|
1022 | |
---|
1023 | if (pSequence && (strlen(pSequence) >= ArbMIN_PROBE_LENGTH)) { |
---|
1024 | ArbProbe *pNewProbe = new ArbProbe(pName, pSequence); |
---|
1025 | |
---|
1026 | if (pNewProbe != 0) { |
---|
1027 | ProbeList.push_back(pNewProbe); |
---|
1028 | |
---|
1029 | if (ppProbe != 0) *ppProbe = pNewProbe; |
---|
1030 | |
---|
1031 | HasChanged = true; |
---|
1032 | bAdded = true; |
---|
1033 | } |
---|
1034 | } |
---|
1035 | |
---|
1036 | return (bAdded); |
---|
1037 | } |
---|
1038 | |
---|
1039 | bool ArbProbeCollection::replace(const char *oldSequence, const char *pName, const char *pSequence, const ArbProbe **ppProbe) { |
---|
1040 | bool bReplaced = false; |
---|
1041 | |
---|
1042 | if (oldSequence && pSequence && (strlen(pSequence) >= ArbMIN_PROBE_LENGTH)) { |
---|
1043 | ArbProbePtrListIter found = find_if(ProbeList.begin(), ProbeList.end(), hasSequence(oldSequence)); |
---|
1044 | if (found != ProbeList.end()) { |
---|
1045 | (*found)->free(); |
---|
1046 | *found = new ArbProbe(pName, pSequence); |
---|
1047 | |
---|
1048 | if (ppProbe != 0) *ppProbe = *found; |
---|
1049 | |
---|
1050 | HasChanged = true; |
---|
1051 | bReplaced = true; |
---|
1052 | } |
---|
1053 | } |
---|
1054 | |
---|
1055 | return (bReplaced); |
---|
1056 | } |
---|
1057 | |
---|
1058 | |
---|
1059 | // ---------------------------------------------------------------------------- |
---|
1060 | |
---|
1061 | bool ArbProbeCollection::remove(const char *pSequence) { |
---|
1062 | bool bRemoved = false; |
---|
1063 | |
---|
1064 | if (pSequence != 0) { |
---|
1065 | ArbProbePtrListIter Iter; |
---|
1066 | std::string rSequence(pSequence); |
---|
1067 | |
---|
1068 | for (Iter = ProbeList.begin() ; Iter != ProbeList.end() ; ++Iter) { |
---|
1069 | ArbProbe *pTestProbe = *Iter; |
---|
1070 | |
---|
1071 | if ((pTestProbe != 0) && (pTestProbe->sequence() == rSequence)) { |
---|
1072 | ProbeList.erase(Iter); |
---|
1073 | |
---|
1074 | pTestProbe->free(); |
---|
1075 | |
---|
1076 | HasChanged = true; |
---|
1077 | bRemoved = true; |
---|
1078 | break; |
---|
1079 | } |
---|
1080 | } |
---|
1081 | } |
---|
1082 | |
---|
1083 | return (bRemoved); |
---|
1084 | } |
---|
1085 | |
---|
1086 | // ---------------------------------------------------------------------------- |
---|
1087 | |
---|
1088 | bool ArbProbeCollection::clear() { |
---|
1089 | bool bClear = false; |
---|
1090 | |
---|
1091 | if (ProbeList.size() > 0) { |
---|
1092 | flush(); |
---|
1093 | |
---|
1094 | HasChanged = true; |
---|
1095 | bClear = true; |
---|
1096 | } |
---|
1097 | |
---|
1098 | return (bClear); |
---|
1099 | } |
---|
1100 | |
---|
1101 | // ---------------------------------------------------------------------------- |
---|
1102 | |
---|
1103 | void ArbProbeCollection::name(const char *pName) { // REFCOUNT_HACK |
---|
1104 | if (pName != 0) { |
---|
1105 | Name = pName; |
---|
1106 | } |
---|
1107 | else { |
---|
1108 | Name = ""; |
---|
1109 | } |
---|
1110 | |
---|
1111 | HasChanged = true; |
---|
1112 | } |
---|
1113 | |
---|
1114 | |
---|
1115 | // ---------------------------------------------------------------------------- |
---|
1116 | // ArbMatchResult method implementations |
---|
1117 | // ---------------------------------------------------------------------------- |
---|
1118 | ArbMatchResult::ArbMatchResult() |
---|
1119 | : ArbRefCount(), |
---|
1120 | CachedResultA(), |
---|
1121 | CachedResultB() |
---|
1122 | { |
---|
1123 | Probe = 0; |
---|
1124 | Weight = 0.0; |
---|
1125 | Padding = 0; |
---|
1126 | Index = 0; |
---|
1127 | } |
---|
1128 | |
---|
1129 | // ---------------------------------------------------------------------------- |
---|
1130 | |
---|
1131 | ArbMatchResult::ArbMatchResult(const ArbProbe *pProbe, const char *pResult, int nSplitPoint, double dWeight) |
---|
1132 | : ArbRefCount(), |
---|
1133 | CachedResultA(), |
---|
1134 | CachedResultB() |
---|
1135 | { |
---|
1136 | ArbStringCache& g_string_cache = get_string_cache(); |
---|
1137 | g_string_cache.saveString(pResult, nSplitPoint, CachedResultA); |
---|
1138 | g_string_cache.saveString(pResult + nSplitPoint, CachedResultB); |
---|
1139 | |
---|
1140 | Probe = pProbe; |
---|
1141 | Weight = dWeight; |
---|
1142 | Padding = 0; |
---|
1143 | Index = 0; |
---|
1144 | |
---|
1145 | if (Probe != 0) { |
---|
1146 | Probe->lock(); |
---|
1147 | } |
---|
1148 | } |
---|
1149 | |
---|
1150 | // ---------------------------------------------------------------------------- |
---|
1151 | |
---|
1152 | ArbMatchResult::ArbMatchResult(const ArbMatchResult& rCopy) |
---|
1153 | : ArbRefCount(), |
---|
1154 | CachedResultA(rCopy.CachedResultA), |
---|
1155 | CachedResultB(rCopy.CachedResultB) |
---|
1156 | { |
---|
1157 | Probe = rCopy.Probe; |
---|
1158 | Weight = rCopy.Weight; |
---|
1159 | Padding = rCopy.Padding; |
---|
1160 | Index = rCopy.Index; |
---|
1161 | |
---|
1162 | if (Probe != 0) { |
---|
1163 | Probe->lock(); |
---|
1164 | } |
---|
1165 | } |
---|
1166 | |
---|
1167 | // ---------------------------------------------------------------------------- |
---|
1168 | |
---|
1169 | ArbMatchResult::~ArbMatchResult() { |
---|
1170 | if (Probe != 0) { |
---|
1171 | Probe->free(); |
---|
1172 | } |
---|
1173 | } |
---|
1174 | |
---|
1175 | // ---------------------------------------------------------------------------- |
---|
1176 | |
---|
1177 | ArbMatchResult& ArbMatchResult::operator = (const ArbMatchResult& rCopy) { |
---|
1178 | Probe = rCopy.Probe; |
---|
1179 | CachedResultA = rCopy.CachedResultA; |
---|
1180 | CachedResultB = rCopy.CachedResultB; |
---|
1181 | Padding = rCopy.Padding; |
---|
1182 | Weight = rCopy.Weight; |
---|
1183 | |
---|
1184 | if (Probe != 0) { |
---|
1185 | Probe->lock(); |
---|
1186 | } |
---|
1187 | |
---|
1188 | return (*this); |
---|
1189 | } |
---|
1190 | |
---|
1191 | // ---------------------------------------------------------------------------- |
---|
1192 | |
---|
1193 | void ArbMatchResult::addedHeadline(std::string& rHeadline) { |
---|
1194 | rHeadline = "---error--probe-----------------"; |
---|
1195 | } |
---|
1196 | |
---|
1197 | // ---------------------------------------------------------------------------- |
---|
1198 | |
---|
1199 | void ArbMatchResult::weightAndResult(std::string& rDest) const { |
---|
1200 | char sBuffer[64] = {0}; |
---|
1201 | std::string sResult; |
---|
1202 | |
---|
1203 | result(sResult); |
---|
1204 | sprintf(sBuffer, "%8g %22.22s ", Weight, Probe != 0 ? Probe->name().c_str() : ""); |
---|
1205 | |
---|
1206 | rDest = sBuffer; |
---|
1207 | rDest += sResult; |
---|
1208 | } |
---|
1209 | |
---|
1210 | // ---------------------------------------------------------------------------- |
---|
1211 | |
---|
1212 | void ArbMatchResult::result(std::string& sResult) const { |
---|
1213 | std::string sResultA; |
---|
1214 | std::string sResultB; |
---|
1215 | |
---|
1216 | ArbStringCache& g_string_cache = get_string_cache(); |
---|
1217 | g_string_cache.loadString(sResultA, CachedResultA); |
---|
1218 | g_string_cache.loadString(sResultB, CachedResultB); |
---|
1219 | |
---|
1220 | sResult.append(sResultA); |
---|
1221 | |
---|
1222 | if (Padding > 0) { |
---|
1223 | sResult.append(Padding, ' '); |
---|
1224 | } |
---|
1225 | |
---|
1226 | sResult.append(sResultB); |
---|
1227 | } |
---|
1228 | |
---|
1229 | |
---|
1230 | // ---------------------------------------------------------------------------- |
---|
1231 | // ArbMatchResultSet method implementations |
---|
1232 | // ---------------------------------------------------------------------------- |
---|
1233 | void ArbMatchResultSet::flush() { |
---|
1234 | ArbMatchResultPtrByStringMultiMapIter Iter; |
---|
1235 | |
---|
1236 | for (Iter = ResultMap.begin() ; Iter != ResultMap.end() ; ++Iter) { |
---|
1237 | ArbMatchResult *pResult = (*Iter).second; |
---|
1238 | |
---|
1239 | if (pResult != 0) { |
---|
1240 | pResult->free(); |
---|
1241 | } |
---|
1242 | } |
---|
1243 | |
---|
1244 | ResultMap.clear(); |
---|
1245 | CommentList.clear(); |
---|
1246 | |
---|
1247 | Headline = ""; |
---|
1248 | EndFullName = 0; |
---|
1249 | } |
---|
1250 | |
---|
1251 | // ---------------------------------------------------------------------------- |
---|
1252 | |
---|
1253 | void ArbMatchResultSet::copy(const ArbMatchResultPtrByStringMultiMap& rMap) { |
---|
1254 | ArbMatchResultPtrByStringMultiMapConstIter Iter; |
---|
1255 | |
---|
1256 | for (Iter = rMap.begin() ; Iter != rMap.end() ; ++Iter) { |
---|
1257 | const std::string& sKey = (*Iter).first; |
---|
1258 | const ArbMatchResult *pResult = (*Iter).second; |
---|
1259 | |
---|
1260 | if (pResult != 0) { |
---|
1261 | ArbMatchResult *pCopy = new ArbMatchResult(*pResult); |
---|
1262 | |
---|
1263 | if (pCopy != 0) { |
---|
1264 | ResultMap.insert(ArbMatchResultPtrStringPair(sKey, pCopy)); |
---|
1265 | } |
---|
1266 | } |
---|
1267 | } |
---|
1268 | |
---|
1269 | ResultMap.clear(); |
---|
1270 | CommentList.clear(); |
---|
1271 | } |
---|
1272 | |
---|
1273 | // ---------------------------------------------------------------------------- |
---|
1274 | |
---|
1275 | ArbMatchResultSet::ArbMatchResultSet() |
---|
1276 | : ArbRefCount(), |
---|
1277 | Headline(), |
---|
1278 | ResultMap(), |
---|
1279 | CommentList() |
---|
1280 | { |
---|
1281 | Probe = 0; |
---|
1282 | Index = 0; |
---|
1283 | EndFullName = 0; |
---|
1284 | } |
---|
1285 | |
---|
1286 | // ---------------------------------------------------------------------------- |
---|
1287 | |
---|
1288 | ArbMatchResultSet::ArbMatchResultSet(const ArbProbe *pProbe) |
---|
1289 | : ArbRefCount(), |
---|
1290 | Headline(), |
---|
1291 | ResultMap(), |
---|
1292 | CommentList() |
---|
1293 | { |
---|
1294 | Probe = 0; |
---|
1295 | Index = 0; |
---|
1296 | EndFullName = 0; |
---|
1297 | |
---|
1298 | initialise(pProbe, 0); |
---|
1299 | } |
---|
1300 | |
---|
1301 | // ---------------------------------------------------------------------------- |
---|
1302 | |
---|
1303 | ArbMatchResultSet::ArbMatchResultSet(const ArbMatchResultSet& rCopy) |
---|
1304 | : ArbRefCount(), |
---|
1305 | Headline(rCopy.Headline.c_str()), |
---|
1306 | ResultMap(), |
---|
1307 | CommentList(rCopy.CommentList) |
---|
1308 | { |
---|
1309 | Probe = 0; |
---|
1310 | Index = 0; |
---|
1311 | EndFullName = 0; |
---|
1312 | |
---|
1313 | initialise(rCopy.Probe, rCopy.Index); |
---|
1314 | copy(rCopy.ResultMap); |
---|
1315 | |
---|
1316 | EndFullName = rCopy.EndFullName; |
---|
1317 | } |
---|
1318 | |
---|
1319 | // ---------------------------------------------------------------------------- |
---|
1320 | |
---|
1321 | ArbMatchResultSet::~ArbMatchResultSet() { |
---|
1322 | flush(); |
---|
1323 | |
---|
1324 | if (Probe != 0) { |
---|
1325 | Probe->free(); |
---|
1326 | } |
---|
1327 | } |
---|
1328 | |
---|
1329 | // ---------------------------------------------------------------------------- |
---|
1330 | |
---|
1331 | void ArbMatchResultSet::initialise(const ArbProbe *pProbe, int nIndex) { |
---|
1332 | Probe = pProbe; |
---|
1333 | Index = nIndex; |
---|
1334 | |
---|
1335 | if (Probe != 0) { |
---|
1336 | Probe->lock(); |
---|
1337 | } |
---|
1338 | |
---|
1339 | flush(); |
---|
1340 | } |
---|
1341 | |
---|
1342 | // ---------------------------------------------------------------------------- |
---|
1343 | |
---|
1344 | bool ArbMatchResultSet::add(const char *pName, |
---|
1345 | const char *pFullName, |
---|
1346 | const char *pMatchPart, |
---|
1347 | const char *pResult, |
---|
1348 | const ArbProbeMatchWeighting& rMatchWeighting) |
---|
1349 | { |
---|
1350 | bool bAdded = false; |
---|
1351 | |
---|
1352 | if ((pResult != 0) && |
---|
1353 | (pName != 0) && |
---|
1354 | (pFullName != 0) && |
---|
1355 | (pMatchPart != 0) && |
---|
1356 | (Probe != 0) && |
---|
1357 | (Probe->sequence().length() > 0)) |
---|
1358 | { |
---|
1359 | double dWeight; |
---|
1360 | const char *pMatchStart = pMatchPart; |
---|
1361 | bool bContinue = true; |
---|
1362 | std::string sKey(pName); |
---|
1363 | ArbMatchResult *pMatchResult; |
---|
1364 | |
---|
1365 | while (bContinue) { |
---|
1366 | switch (*pMatchStart) { |
---|
1367 | case '-': { |
---|
1368 | pMatchStart++; |
---|
1369 | |
---|
1370 | bContinue = false; |
---|
1371 | break; |
---|
1372 | } |
---|
1373 | |
---|
1374 | case '\0': |
---|
1375 | case '=': { |
---|
1376 | bContinue = false; |
---|
1377 | break; |
---|
1378 | } |
---|
1379 | |
---|
1380 | default: { |
---|
1381 | pMatchStart++; |
---|
1382 | |
---|
1383 | bContinue = true; |
---|
1384 | } |
---|
1385 | } |
---|
1386 | } |
---|
1387 | |
---|
1388 | dWeight = rMatchWeighting.matchWeightResult(Probe->sequence().c_str(), pMatchStart); |
---|
1389 | pMatchResult = new ArbMatchResult(Probe, pResult, EndFullName, dWeight); |
---|
1390 | |
---|
1391 | if (pMatchResult != 0) { |
---|
1392 | pMatchResult->index(Index); |
---|
1393 | ResultMap.insert(ArbMatchResultPtrStringPair(sKey, pMatchResult)); |
---|
1394 | |
---|
1395 | bAdded = true; |
---|
1396 | } |
---|
1397 | } |
---|
1398 | |
---|
1399 | return (bAdded); |
---|
1400 | } |
---|
1401 | |
---|
1402 | // ---------------------------------------------------------------------------- |
---|
1403 | |
---|
1404 | bool ArbMatchResultSet::isMatched(const ArbStringList& rCladeList, |
---|
1405 | bool& bPartialMatch, |
---|
1406 | double dThreshold, |
---|
1407 | double dCladeMarkedThreshold, |
---|
1408 | double dCladePartiallyMarkedThreshold) const |
---|
1409 | { |
---|
1410 | bool bMatched = false; |
---|
1411 | int nCladeSize = rCladeList.size(); |
---|
1412 | |
---|
1413 | if (nCladeSize > 0) { |
---|
1414 | int nMatchedSize = (int)(nCladeSize * dCladeMarkedThreshold + 0.5); |
---|
1415 | int nPartiallyMatchedSize = (int)(nCladeSize * dCladePartiallyMarkedThreshold + 0.5); |
---|
1416 | int nMatchedCount = 0; |
---|
1417 | |
---|
1418 | for (ArbStringListConstIter Iter = rCladeList.begin() ; Iter != rCladeList.end() ; ++Iter) { |
---|
1419 | const std::string& rName = *Iter; |
---|
1420 | |
---|
1421 | if (isMatched(rName, dThreshold)) { |
---|
1422 | nMatchedCount++; |
---|
1423 | } |
---|
1424 | } |
---|
1425 | |
---|
1426 | bMatched = (nMatchedCount >= nMatchedSize); |
---|
1427 | bPartialMatch = false; |
---|
1428 | |
---|
1429 | // Only check for partial match if we don't have a match. If a partial |
---|
1430 | // match is found then isMatched() should return true. |
---|
1431 | if (!bMatched) { |
---|
1432 | bPartialMatch = (nMatchedCount >= nPartiallyMatchedSize); |
---|
1433 | bMatched = bPartialMatch; |
---|
1434 | } |
---|
1435 | } |
---|
1436 | |
---|
1437 | return (bMatched); |
---|
1438 | } |
---|
1439 | |
---|
1440 | // ---------------------------------------------------------------------------- |
---|
1441 | |
---|
1442 | bool ArbMatchResultSet::isMatched(const std::string& rName, double dThreshold) const { |
---|
1443 | bool bMatched = false; |
---|
1444 | |
---|
1445 | ArbMatchResultPtrByStringMultiMapConstIter Iter = ResultMap.find(rName); |
---|
1446 | |
---|
1447 | if (Iter != ResultMap.end()) { |
---|
1448 | const ArbMatchResult *pResult = (*Iter).second; |
---|
1449 | |
---|
1450 | bMatched = pResult->weight() <= dThreshold; |
---|
1451 | } |
---|
1452 | |
---|
1453 | return (bMatched); |
---|
1454 | } |
---|
1455 | |
---|
1456 | // ---------------------------------------------------------------------------- |
---|
1457 | |
---|
1458 | bool ArbMatchResultSet::addComment(const char *pComment) { |
---|
1459 | bool bAdded = false; |
---|
1460 | |
---|
1461 | if ((pComment != 0) && |
---|
1462 | (Probe != 0) && |
---|
1463 | (Probe->sequence().length() > 0)) |
---|
1464 | { |
---|
1465 | CommentList.push_back(std::string(pComment)); |
---|
1466 | |
---|
1467 | bAdded = true; |
---|
1468 | } |
---|
1469 | |
---|
1470 | return (bAdded); |
---|
1471 | } |
---|
1472 | |
---|
1473 | // ---------------------------------------------------------------------------- |
---|
1474 | |
---|
1475 | void ArbMatchResultSet::findMaximumWeight(double& dMaximumWeight) const { |
---|
1476 | ArbMatchResultPtrByStringMultiMapConstIter Iter; |
---|
1477 | |
---|
1478 | for (Iter = ResultMap.begin() ; Iter != ResultMap.end() ; ++Iter) { |
---|
1479 | const ArbMatchResult *pResult = (*Iter).second; |
---|
1480 | |
---|
1481 | if ((pResult != 0) && (dMaximumWeight < pResult->weight())) { |
---|
1482 | dMaximumWeight = pResult->weight(); |
---|
1483 | } |
---|
1484 | } |
---|
1485 | } |
---|
1486 | |
---|
1487 | // ---------------------------------------------------------------------------- |
---|
1488 | |
---|
1489 | void ArbMatchResultSet::enumerateResults(ArbMatchResultPtrByDoubleMultiMap& rMap, int nMaxFullName) { |
---|
1490 | ArbMatchResultPtrByStringMultiMapIter Iter; |
---|
1491 | |
---|
1492 | for (Iter = ResultMap.begin() ; Iter != ResultMap.end() ; ++Iter) { |
---|
1493 | ArbMatchResult *pResult = (*Iter).second; |
---|
1494 | |
---|
1495 | if (pResult != 0) { |
---|
1496 | pResult->padding(nMaxFullName - EndFullName); |
---|
1497 | rMap.insert(ArbMatchResultPtrDoublePair(pResult->weight(), pResult)); |
---|
1498 | } |
---|
1499 | } |
---|
1500 | } |
---|
1501 | |
---|
1502 | |
---|
1503 | // ---------------------------------------------------------------------------- |
---|
1504 | // ArbMatchResultsManager method implementations |
---|
1505 | // ---------------------------------------------------------------------------- |
---|
1506 | void ArbMatchResultsManager::flush() { |
---|
1507 | ArbMatchResultPtrByStringMultiMapIter Iter; |
---|
1508 | |
---|
1509 | for (Iter = ResultsMap.begin() ; Iter != ResultsMap.end() ; ++Iter) { |
---|
1510 | ArbMatchResult *pMatchResult = (*Iter).second; |
---|
1511 | |
---|
1512 | if (pMatchResult != 0) { |
---|
1513 | pMatchResult->free(); |
---|
1514 | } |
---|
1515 | } |
---|
1516 | |
---|
1517 | ResultsMap.clear(); |
---|
1518 | } |
---|
1519 | |
---|
1520 | // ---------------------------------------------------------------------------- |
---|
1521 | |
---|
1522 | void ArbMatchResultsManager::initFileName() { |
---|
1523 | char *uniqueName = GB_unique_filename("ArbMatchResults", "txt"); |
---|
1524 | char *pTmpFileName = GB_create_tempfile(uniqueName); |
---|
1525 | |
---|
1526 | if (pTmpFileName != 0) { |
---|
1527 | ResultsFileName = pTmpFileName; |
---|
1528 | } |
---|
1529 | |
---|
1530 | free(pTmpFileName); |
---|
1531 | free(uniqueName); |
---|
1532 | } |
---|
1533 | |
---|
1534 | // ---------------------------------------------------------------------------- |
---|
1535 | |
---|
1536 | ArbMatchResultsManager::ArbMatchResultsManager() |
---|
1537 | : ResultsMap(), |
---|
1538 | ResultSetMap(), |
---|
1539 | ResultsFileName() |
---|
1540 | { |
---|
1541 | MaximumWeight = 0.0; |
---|
1542 | initFileName(); |
---|
1543 | } |
---|
1544 | |
---|
1545 | // ---------------------------------------------------------------------------- |
---|
1546 | |
---|
1547 | ArbMatchResultsManager::ArbMatchResultsManager(const ArbMatchResultsManager& rCopy) |
---|
1548 | : ResultsMap(), |
---|
1549 | ResultSetMap(rCopy.ResultSetMap), |
---|
1550 | ResultsFileName() |
---|
1551 | { |
---|
1552 | MaximumWeight = rCopy.MaximumWeight; |
---|
1553 | updateResults(); |
---|
1554 | initFileName(); |
---|
1555 | } |
---|
1556 | |
---|
1557 | // ---------------------------------------------------------------------------- |
---|
1558 | |
---|
1559 | ArbMatchResultsManager::~ArbMatchResultsManager() { |
---|
1560 | ResultSetMap.clear(); |
---|
1561 | flush(); |
---|
1562 | |
---|
1563 | if (ResultsFileName.length() > 0) { |
---|
1564 | unlink(ResultsFileName.c_str()); |
---|
1565 | } |
---|
1566 | |
---|
1567 | // This assumes that there is only ever on instance of ArbMatchResultsManager |
---|
1568 | // which is true at the moment. Slightly dodgey but it will stop the cache |
---|
1569 | // file from ballooning out too much. |
---|
1570 | get_string_cache().flush(); |
---|
1571 | } |
---|
1572 | |
---|
1573 | // ---------------------------------------------------------------------------- |
---|
1574 | |
---|
1575 | void ArbMatchResultsManager::reset() { |
---|
1576 | ResultSetMap.clear(); |
---|
1577 | flush(); |
---|
1578 | |
---|
1579 | if (ResultsFileName.length() > 0) { |
---|
1580 | unlink(ResultsFileName.c_str()); |
---|
1581 | } |
---|
1582 | |
---|
1583 | // This assumes that there is only ever on instance of ArbMatchResultsManager |
---|
1584 | // which is true at the moment. Slightly dodgey but it will stop the cache |
---|
1585 | // file from ballooning out too much. |
---|
1586 | get_string_cache().flush(); |
---|
1587 | } |
---|
1588 | |
---|
1589 | // ---------------------------------------------------------------------------- |
---|
1590 | |
---|
1591 | ArbMatchResultSet *ArbMatchResultsManager::addResultSet(const ArbProbe *pProbe) { |
---|
1592 | ArbMatchResultSet *pResultSet = 0; |
---|
1593 | |
---|
1594 | if (pProbe != 0) { |
---|
1595 | pResultSet = (ArbMatchResultSet*)findResultSet(pProbe->sequence().c_str()); |
---|
1596 | |
---|
1597 | if (pResultSet == 0) { |
---|
1598 | ResultSetMap[pProbe->sequence()] = ArbMatchResultSet(); |
---|
1599 | |
---|
1600 | pResultSet = (ArbMatchResultSet*)findResultSet(pProbe->sequence().c_str()); |
---|
1601 | } |
---|
1602 | } |
---|
1603 | |
---|
1604 | return (pResultSet); |
---|
1605 | } |
---|
1606 | |
---|
1607 | // ---------------------------------------------------------------------------- |
---|
1608 | |
---|
1609 | const ArbMatchResultSet *ArbMatchResultsManager::findResultSet(const char *pProbeSequence) const { |
---|
1610 | const ArbMatchResultSet *pResultSet = 0; |
---|
1611 | |
---|
1612 | if (pProbeSequence != 0) { |
---|
1613 | ArbMatchResultSetByStringMapConstIter Iter = ResultSetMap.find(std::string(pProbeSequence)); |
---|
1614 | |
---|
1615 | if (Iter != ResultSetMap.end()) { |
---|
1616 | pResultSet = &((*Iter).second); |
---|
1617 | } |
---|
1618 | } |
---|
1619 | |
---|
1620 | return (pResultSet); |
---|
1621 | } |
---|
1622 | |
---|
1623 | // ---------------------------------------------------------------------------- |
---|
1624 | |
---|
1625 | void ArbMatchResultsManager::updateResults() { |
---|
1626 | ArbMatchResultSetByStringMapIter Iter; |
---|
1627 | ArbMatchResultPtrByStringMultiMapConstIter IterR; |
---|
1628 | |
---|
1629 | flush(); |
---|
1630 | |
---|
1631 | MaximumWeight = 0.0; |
---|
1632 | |
---|
1633 | for (Iter = ResultSetMap.begin() ; Iter != ResultSetMap.end() ; ++Iter) { |
---|
1634 | ArbMatchResultSet& rMatchResultSet = (*Iter).second; |
---|
1635 | |
---|
1636 | rMatchResultSet.findMaximumWeight(MaximumWeight); |
---|
1637 | |
---|
1638 | for (IterR = rMatchResultSet.resultMap().begin() ; IterR != rMatchResultSet.resultMap().end() ; ++IterR) { |
---|
1639 | const std::string& rKey = (*IterR).first; |
---|
1640 | const ArbMatchResult *pMatchResult = (*IterR).second; |
---|
1641 | |
---|
1642 | pMatchResult->lock(); |
---|
1643 | ResultsMap.insert(ArbMatchResultPtrStringPair(rKey, (ArbMatchResult*)pMatchResult)); |
---|
1644 | } |
---|
1645 | } |
---|
1646 | } |
---|
1647 | |
---|
1648 | // ---------------------------------------------------------------------------- |
---|
1649 | |
---|
1650 | int ArbMatchResultsManager::enumerate_results(ArbMatchResultsEnumCallback pCallback, void *pContext) { |
---|
1651 | int nResults = 0; |
---|
1652 | |
---|
1653 | bool bAborted = false; |
---|
1654 | |
---|
1655 | if (pCallback != 0) { |
---|
1656 | ArbMatchResultPtrByDoubleMultiMap rResultsMap; |
---|
1657 | |
---|
1658 | // Need to compile the results sorted in ascending match weight. |
---|
1659 | ArbMatchResultSetByStringMapIter Iter; |
---|
1660 | int nItem = 0; |
---|
1661 | int nItems = 1; |
---|
1662 | int nMaxFullName = 0; |
---|
1663 | std::string sHeadline; |
---|
1664 | |
---|
1665 | for (Iter = ResultSetMap.begin() ; (Iter != ResultSetMap.end()) && !bAborted ; ++Iter) { |
---|
1666 | ArbMatchResultSet& rMatchResultSet = (*Iter).second; |
---|
1667 | |
---|
1668 | if (rMatchResultSet.endFullName() > nMaxFullName) { |
---|
1669 | ArbMatchResult::addedHeadline(sHeadline); |
---|
1670 | |
---|
1671 | sHeadline += rMatchResultSet.headline(); |
---|
1672 | nMaxFullName = rMatchResultSet.endFullName(); |
---|
1673 | } |
---|
1674 | } |
---|
1675 | |
---|
1676 | if (pCallback(pContext, sHeadline.c_str(), true, nItem, nItems)) { |
---|
1677 | bAborted = true; |
---|
1678 | } |
---|
1679 | |
---|
1680 | for (Iter = ResultSetMap.begin() ; (Iter != ResultSetMap.end()) && !bAborted ; ++Iter) { |
---|
1681 | ArbMatchResultSet& rMatchResultSet = (*Iter).second; |
---|
1682 | |
---|
1683 | rMatchResultSet.enumerateResults(rResultsMap, nMaxFullName); |
---|
1684 | |
---|
1685 | ArbStringListConstIter CommentIter; |
---|
1686 | |
---|
1687 | for (CommentIter = rMatchResultSet.commentList().begin() ; |
---|
1688 | CommentIter != rMatchResultSet.commentList().begin() ; |
---|
1689 | ++CommentIter) |
---|
1690 | { |
---|
1691 | const std::string& rComment = *CommentIter; |
---|
1692 | |
---|
1693 | if (pCallback(pContext, rComment.c_str(), true, nItem, nItems)) { |
---|
1694 | bAborted = true; |
---|
1695 | break; |
---|
1696 | } |
---|
1697 | } |
---|
1698 | } |
---|
1699 | |
---|
1700 | ArbMatchResultPtrByDoubleMultiMapIter ResIter; |
---|
1701 | |
---|
1702 | nItems = rResultsMap.size(); |
---|
1703 | |
---|
1704 | for (ResIter = rResultsMap.begin() ; (ResIter != rResultsMap.end()) && !bAborted ; ++ResIter) { |
---|
1705 | const ArbMatchResult *pResult = (*ResIter).second; |
---|
1706 | |
---|
1707 | if (pResult != 0) { |
---|
1708 | std::string sResult; |
---|
1709 | |
---|
1710 | pResult->weightAndResult(sResult); |
---|
1711 | |
---|
1712 | if (pCallback(pContext, sResult.c_str(), false, nItem, nItems)) { |
---|
1713 | bAborted = true; |
---|
1714 | break; |
---|
1715 | } |
---|
1716 | |
---|
1717 | nResults++; |
---|
1718 | nItem++; |
---|
1719 | } |
---|
1720 | } |
---|
1721 | } |
---|
1722 | |
---|
1723 | return (nResults); |
---|
1724 | } |
---|
1725 | |
---|
1726 | // ---------------------------------------------------------------------------- |
---|
1727 | |
---|
1728 | const char *ArbMatchResultsManager::resultsFileName() const { |
---|
1729 | return (ResultsFileName.c_str()); |
---|
1730 | } |
---|
1731 | |
---|
1732 | // ---------------------------------------------------------------------------- |
---|
1733 | |
---|
1734 | void ArbMatchResultsManager::openResultsFile() const { |
---|
1735 | pid_t pid = fork(); |
---|
1736 | |
---|
1737 | if (pid == 0) { |
---|
1738 | // We are the child process. Execute system command to open the file. |
---|
1739 | std::string sCommand("\"xdg-open "); |
---|
1740 | |
---|
1741 | sCommand += ResultsFileName; |
---|
1742 | sCommand += "\""; |
---|
1743 | |
---|
1744 | execl("/bin/sh", sCommand.c_str(), (char *)0); |
---|
1745 | exit(0); |
---|
1746 | } |
---|
1747 | } |
---|