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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/* -*- c-basic-offset: 4; indent-tabs-mode: nil -*- */</span></div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> <span class="comment">/* ====================================================================</span></div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> <span class="comment"> * Copyright (c) 1999-2004 Carnegie Mellon University. All rights</span></div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment"> * reserved.</span></div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> <span class="comment"> *</span></div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> <span class="comment"> * Redistribution and use in source and binary forms, with or without</span></div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> <span class="comment"> * modification, are permitted provided that the following conditions</span></div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> <span class="comment"> * are met:</span></div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> <span class="comment"> *</span></div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> <span class="comment"> * 1. Redistributions of source code must retain the above copyright</span></div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> <span class="comment"> * notice, this list of conditions and the following disclaimer. </span></div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> <span class="comment"> *</span></div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> <span class="comment"> * 2. Redistributions in binary form must reproduce the above copyright</span></div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> <span class="comment"> * notice, this list of conditions and the following disclaimer in</span></div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> <span class="comment"> * the documentation and/or other materials provided with the</span></div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> <span class="comment"> * distribution.</span></div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> <span class="comment"> *</span></div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> <span class="comment"> * This work was supported in part by funding from the Defense Advanced </span></div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> <span class="comment"> * Research Projects Agency and the National Science Foundation of the </span></div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> <span class="comment"> * United States of America, and the CMU Sphinx Speech Consortium.</span></div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> <span class="comment"> *</span></div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> <span class="comment"> * THIS SOFTWARE IS PROVIDED BY CARNEGIE MELLON UNIVERSITY ``AS IS'' AND </span></div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> <span class="comment"> * ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, </span></div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> <span class="comment"> * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR</span></div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> <span class="comment"> * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CARNEGIE MELLON UNIVERSITY</span></div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> <span class="comment"> * NOR ITS EMPLOYEES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,</span></div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> <span class="comment"> * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT </span></div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> <span class="comment"> * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, </span></div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> <span class="comment"> * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY </span></div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> <span class="comment"> * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT </span></div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span> <span class="comment"> * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE </span></div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span> <span class="comment"> * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span> <span class="comment"> *</span></div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span> <span class="comment"> * ====================================================================</span></div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span> <span class="comment"> *</span></div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> <span class="comment"> */</span></div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> </div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> <span class="comment">/* System headers. */</span></div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> <span class="preprocessor">#include <assert.h></span></div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> <span class="preprocessor">#include <stdlib.h></span></div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> <span class="preprocessor">#include <string.h></span></div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> <span class="preprocessor">#include <limits.h></span></div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> <span class="comment">/* SphinxBase headers. */</span></div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> <span class="preprocessor">#include <sphinxbase/ckd_alloc.h></span></div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> <span class="preprocessor">#include <sphinxbase/err.h></span></div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> <span class="comment">/* Local headers. */</span></div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> <span class="preprocessor">#include "<a class="code" href="hmm_8h.html">hmm.h</a>"</span></div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> </div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> <a class="code" href="structhmm__context__t.html">hmm_context_t</a> *</div><div class="line"><a name="l00056"></a><span class="lineno"><a class="line" href="hmm_8h.html#a4d6e2799cbe290112e8517adcab1b038"> 56</a></span> <a class="code" href="hmm_8h.html#a4d6e2799cbe290112e8517adcab1b038">hmm_context_init</a>(int32 n_emit_state,</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  uint8 ** <span class="keyword">const</span> *tp,</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  int16 <span class="keyword">const</span> *senscore,</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span>  uint16 * <span class="keyword">const</span> *sseq)</div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> {</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  <a class="code" href="structhmm__context__t.html">hmm_context_t</a> *ctx;</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> </div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span>  assert(n_emit_state > 0);</div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span>  <span class="keywordflow">if</span> (n_emit_state > <a class="code" href="hmm_8h.html#a1eb055ab0e55008f27d78e7b07a55a1c">HMM_MAX_NSTATE</a>) {</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span>  E_ERROR(<span class="stringliteral">"Number of emitting states must be <= %d\n"</span>, <a class="code" href="hmm_8h.html#a1eb055ab0e55008f27d78e7b07a55a1c">HMM_MAX_NSTATE</a>);</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span>  <span class="keywordflow">return</span> NULL;</div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span>  }</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span>  ctx = ckd_calloc(1, <span class="keyword">sizeof</span>(*ctx));</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span>  ctx->n_emit_state = n_emit_state;</div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span>  ctx->tp = tp;</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span>  ctx->senscore = senscore;</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span>  ctx->sseq = sseq;</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span>  ctx->st_sen_scr = ckd_calloc(n_emit_state, <span class="keyword">sizeof</span>(*ctx->st_sen_scr));</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span>  <span class="keywordflow">return</span> ctx;</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span> }</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00080"></a><span class="lineno"><a class="line" href="hmm_8h.html#ab66534ad7970d49527f1b2a1e76bb05e"> 80</a></span> <a class="code" href="hmm_8h.html#ab66534ad7970d49527f1b2a1e76bb05e">hmm_context_free</a>(<a class="code" href="structhmm__context__t.html">hmm_context_t</a> *ctx)</div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> {</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span>  <span class="keywordflow">if</span> (ctx == NULL)</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span>  <span class="keywordflow">return</span>;</div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span>  ckd_free(ctx->st_sen_scr);</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span>  ckd_free(ctx);</div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span> }</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00089"></a><span class="lineno"><a class="line" href="hmm_8h.html#aa911ae0d1c0eba562692fbeebca90d78"> 89</a></span> <a class="code" href="hmm_8h.html#aa911ae0d1c0eba562692fbeebca90d78">hmm_init</a>(<a class="code" href="structhmm__context__t.html">hmm_context_t</a> *ctx, <a class="code" href="structhmm__t.html">hmm_t</a> *hmm, <span class="keywordtype">int</span> mpx, <span class="keywordtype">int</span> ssid, <span class="keywordtype">int</span> tmatid)</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> {</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span>  hmm->ctx = ctx;</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span>  hmm->mpx = mpx;</div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span>  hmm->n_emit_state = ctx->n_emit_state;</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span>  <span class="keywordflow">if</span> (mpx) {</div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span>  <span class="keywordtype">int</span> i;</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  hmm->ssid = <a class="code" href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a>;</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  hmm->senid[0] = ssid;</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span>  <span class="keywordflow">for</span> (i = 1; i < hmm_n_emit_state(hmm); ++i) {</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  hmm->senid[i] = <a class="code" href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a>;</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span>  }</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span>  }</div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span>  hmm->ssid = ssid;</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span>  memcpy(hmm->senid, ctx->sseq[ssid], hmm->n_emit_state * <span class="keyword">sizeof</span>(*hmm->senid));</div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span>  }</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span>  hmm->tmatid = tmatid;</div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span>  <a class="code" href="hmm_8h.html#af4c0cefb23087a0b1731b34048cfdaf9">hmm_clear</a>(hmm);</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span> }</div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span> </div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00111"></a><span class="lineno"><a class="line" href="hmm_8h.html#a7440ced1649225beb6816bf62481e08b"> 111</a></span> <a class="code" href="hmm_8h.html#a7440ced1649225beb6816bf62481e08b">hmm_deinit</a>(<a class="code" href="structhmm__t.html">hmm_t</a> *hmm)</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> {</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> }</div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> </div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00116"></a><span class="lineno"><a class="line" href="hmm_8h.html#ad747fa967b5e414ad48fdffb9b767baf"> 116</a></span> <a class="code" href="hmm_8h.html#ad747fa967b5e414ad48fdffb9b767baf">hmm_dump</a>(<a class="code" href="structhmm__t.html">hmm_t</a> * hmm,</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span>  FILE * fp)</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> {</div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span>  int32 i;</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> </div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span>  <span class="keywordflow">if</span> (hmm_is_mpx(hmm)) {</div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span>  fprintf(fp, <span class="stringliteral">"MPX "</span>);</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span>  <span class="keywordflow">for</span> (i = 0; i < hmm_n_emit_state(hmm); i++)</div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span>  fprintf(fp, <span class="stringliteral">" %11d"</span>, hmm_senid(hmm, i));</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span>  fprintf(fp, <span class="stringliteral">" ( "</span>);</div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span>  <span class="keywordflow">for</span> (i = 0; i < hmm_n_emit_state(hmm); i++)</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span>  fprintf(fp, <span class="stringliteral">"%d "</span>, hmm_ssid(hmm, i));</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span>  fprintf(fp, <span class="stringliteral">")\n"</span>);</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span>  }</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span>  fprintf(fp, <span class="stringliteral">"SSID "</span>);</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  <span class="keywordflow">for</span> (i = 0; i < hmm_n_emit_state(hmm); i++)</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span>  fprintf(fp, <span class="stringliteral">" %11d"</span>, hmm_senid(hmm, i));</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  fprintf(fp, <span class="stringliteral">" (%d)\n"</span>, hmm_ssid(hmm, 0));</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span>  }</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span>  <span class="keywordflow">if</span> (hmm->ctx->senscore) {</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span>  fprintf(fp, <span class="stringliteral">"SENSCR"</span>);</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span>  <span class="keywordflow">for</span> (i = 0; i < hmm_n_emit_state(hmm); i++)</div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span>  fprintf(fp, <span class="stringliteral">" %11d"</span>, hmm_senscr(hmm, i));</div><div class="line"><a name="l00141"></a><span class="lineno"> 141</span>  fprintf(fp, <span class="stringliteral">"\n"</span>);</div><div class="line"><a name="l00142"></a><span class="lineno"> 142</span>  }</div><div class="line"><a name="l00143"></a><span class="lineno"> 143</span> </div><div class="line"><a name="l00144"></a><span class="lineno"> 144</span>  fprintf(fp, <span class="stringliteral">"SCORES %11d"</span>, hmm_in_score(hmm));</div><div class="line"><a name="l00145"></a><span class="lineno"> 145</span>  <span class="keywordflow">for</span> (i = 1; i < hmm_n_emit_state(hmm); i++)</div><div class="line"><a name="l00146"></a><span class="lineno"> 146</span>  fprintf(fp, <span class="stringliteral">" %11d"</span>, hmm_score(hmm, i));</div><div class="line"><a name="l00147"></a><span class="lineno"> 147</span>  fprintf(fp, <span class="stringliteral">" %11d"</span>, hmm_out_score(hmm));</div><div class="line"><a name="l00148"></a><span class="lineno"> 148</span>  fprintf(fp, <span class="stringliteral">"\n"</span>);</div><div class="line"><a name="l00149"></a><span class="lineno"> 149</span> </div><div class="line"><a name="l00150"></a><span class="lineno"> 150</span>  fprintf(fp, <span class="stringliteral">"HISTID %11d"</span>, hmm_in_history(hmm));</div><div class="line"><a name="l00151"></a><span class="lineno"> 151</span>  <span class="keywordflow">for</span> (i = 1; i < hmm_n_emit_state(hmm); i++)</div><div class="line"><a name="l00152"></a><span class="lineno"> 152</span>  fprintf(fp, <span class="stringliteral">" %11d"</span>, hmm_history(hmm, i));</div><div class="line"><a name="l00153"></a><span class="lineno"> 153</span>  fprintf(fp, <span class="stringliteral">" %11d"</span>, hmm_out_history(hmm));</div><div class="line"><a name="l00154"></a><span class="lineno"> 154</span>  fprintf(fp, <span class="stringliteral">"\n"</span>);</div><div class="line"><a name="l00155"></a><span class="lineno"> 155</span> </div><div class="line"><a name="l00156"></a><span class="lineno"> 156</span>  <span class="keywordflow">if</span> (hmm_in_score(hmm) > 0)</div><div class="line"><a name="l00157"></a><span class="lineno"> 157</span>  fprintf(fp,</div><div class="line"><a name="l00158"></a><span class="lineno"> 158</span>  <span class="stringliteral">"ALERT!! The input score %d is large than 0. Probably wrap around.\n"</span>,</div><div class="line"><a name="l00159"></a><span class="lineno"> 159</span>  hmm_in_score(hmm));</div><div class="line"><a name="l00160"></a><span class="lineno"> 160</span>  <span class="keywordflow">if</span> (hmm_out_score(hmm) > 0)</div><div class="line"><a name="l00161"></a><span class="lineno"> 161</span>  fprintf(fp,</div><div class="line"><a name="l00162"></a><span class="lineno"> 162</span>  <span class="stringliteral">"ALERT!! The output score %d is large than 0. Probably wrap around\n."</span>,</div><div class="line"><a name="l00163"></a><span class="lineno"> 163</span>  hmm_out_score(hmm));</div><div class="line"><a name="l00164"></a><span class="lineno"> 164</span> </div><div class="line"><a name="l00165"></a><span class="lineno"> 165</span>  fflush(fp);</div><div class="line"><a name="l00166"></a><span class="lineno"> 166</span> }</div><div class="line"><a name="l00167"></a><span class="lineno"> 167</span> </div><div class="line"><a name="l00168"></a><span class="lineno"> 168</span> </div><div class="line"><a name="l00169"></a><span class="lineno"> 169</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00170"></a><span class="lineno"><a class="line" href="hmm_8h.html#a9561d7ffa1e61c99de2d2b900774152f"> 170</a></span> <a class="code" href="hmm_8h.html#a9561d7ffa1e61c99de2d2b900774152f">hmm_clear_scores</a>(<a class="code" href="structhmm__t.html">hmm_t</a> * h)</div><div class="line"><a name="l00171"></a><span class="lineno"> 171</span> {</div><div class="line"><a name="l00172"></a><span class="lineno"> 172</span>  int32 i;</div><div class="line"><a name="l00173"></a><span class="lineno"> 173</span> </div><div class="line"><a name="l00174"></a><span class="lineno"> 174</span>  hmm_in_score(h) = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00175"></a><span class="lineno"> 175</span>  <span class="keywordflow">for</span> (i = 1; i < hmm_n_emit_state(h); i++)</div><div class="line"><a name="l00176"></a><span class="lineno"> 176</span>  hmm_score(h, i) = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00177"></a><span class="lineno"> 177</span>  hmm_out_score(h) = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00178"></a><span class="lineno"> 178</span> </div><div class="line"><a name="l00179"></a><span class="lineno"> 179</span>  h->bestscore = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00180"></a><span class="lineno"> 180</span> }</div><div class="line"><a name="l00181"></a><span class="lineno"> 181</span> </div><div class="line"><a name="l00182"></a><span class="lineno"> 182</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00183"></a><span class="lineno"><a class="line" href="hmm_8h.html#af4c0cefb23087a0b1731b34048cfdaf9"> 183</a></span> <a class="code" href="hmm_8h.html#af4c0cefb23087a0b1731b34048cfdaf9">hmm_clear</a>(<a class="code" href="structhmm__t.html">hmm_t</a> * h)</div><div class="line"><a name="l00184"></a><span class="lineno"> 184</span> {</div><div class="line"><a name="l00185"></a><span class="lineno"> 185</span>  int32 i;</div><div class="line"><a name="l00186"></a><span class="lineno"> 186</span> </div><div class="line"><a name="l00187"></a><span class="lineno"> 187</span>  hmm_in_score(h) = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00188"></a><span class="lineno"> 188</span>  hmm_in_history(h) = -1;</div><div class="line"><a name="l00189"></a><span class="lineno"> 189</span>  <span class="keywordflow">for</span> (i = 1; i < hmm_n_emit_state(h); i++) {</div><div class="line"><a name="l00190"></a><span class="lineno"> 190</span>  hmm_score(h, i) = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00191"></a><span class="lineno"> 191</span>  hmm_history(h, i) = -1;</div><div class="line"><a name="l00192"></a><span class="lineno"> 192</span>  }</div><div class="line"><a name="l00193"></a><span class="lineno"> 193</span>  hmm_out_score(h) = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00194"></a><span class="lineno"> 194</span>  hmm_out_history(h) = -1;</div><div class="line"><a name="l00195"></a><span class="lineno"> 195</span> </div><div class="line"><a name="l00196"></a><span class="lineno"> 196</span>  h->bestscore = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00197"></a><span class="lineno"> 197</span>  h->frame = -1;</div><div class="line"><a name="l00198"></a><span class="lineno"> 198</span> }</div><div class="line"><a name="l00199"></a><span class="lineno"> 199</span> </div><div class="line"><a name="l00200"></a><span class="lineno"> 200</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00201"></a><span class="lineno"><a class="line" href="hmm_8h.html#a7285d01d533996d750c78e0d96042716"> 201</a></span> <a class="code" href="hmm_8h.html#a7285d01d533996d750c78e0d96042716">hmm_enter</a>(<a class="code" href="structhmm__t.html">hmm_t</a> *h, int32 score, int32 histid, <span class="keywordtype">int</span> frame)</div><div class="line"><a name="l00202"></a><span class="lineno"> 202</span> {</div><div class="line"><a name="l00203"></a><span class="lineno"> 203</span>  hmm_in_score(h) = score;</div><div class="line"><a name="l00204"></a><span class="lineno"> 204</span>  hmm_in_history(h) = histid;</div><div class="line"><a name="l00205"></a><span class="lineno"> 205</span>  hmm_frame(h) = frame;</div><div class="line"><a name="l00206"></a><span class="lineno"> 206</span> }</div><div class="line"><a name="l00207"></a><span class="lineno"> 207</span> </div><div class="line"><a name="l00208"></a><span class="lineno"> 208</span> <span class="keywordtype">void</span></div><div class="line"><a name="l00209"></a><span class="lineno"><a class="line" href="hmm_8h.html#a0438bc7672ff9200274ffe7b5051eb92"> 209</a></span> <a class="code" href="hmm_8h.html#a0438bc7672ff9200274ffe7b5051eb92">hmm_normalize</a>(<a class="code" href="structhmm__t.html">hmm_t</a> *h, int32 bestscr)</div><div class="line"><a name="l00210"></a><span class="lineno"> 210</span> {</div><div class="line"><a name="l00211"></a><span class="lineno"> 211</span>  int32 i;</div><div class="line"><a name="l00212"></a><span class="lineno"> 212</span> </div><div class="line"><a name="l00213"></a><span class="lineno"> 213</span>  <span class="keywordflow">for</span> (i = 0; i < hmm_n_emit_state(h); i++) {</div><div class="line"><a name="l00214"></a><span class="lineno"> 214</span>  <span class="keywordflow">if</span> (hmm_score(h, i) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>)</div><div class="line"><a name="l00215"></a><span class="lineno"> 215</span>  hmm_score(h, i) -= bestscr;</div><div class="line"><a name="l00216"></a><span class="lineno"> 216</span>  }</div><div class="line"><a name="l00217"></a><span class="lineno"> 217</span>  <span class="keywordflow">if</span> (hmm_out_score(h) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>)</div><div class="line"><a name="l00218"></a><span class="lineno"> 218</span>  hmm_out_score(h) -= bestscr;</div><div class="line"><a name="l00219"></a><span class="lineno"> 219</span> }</div><div class="line"><a name="l00220"></a><span class="lineno"> 220</span> </div><div class="line"><a name="l00221"></a><span class="lineno"> 221</span> <span class="preprocessor">#define hmm_tprob_5st(i, j) (-tp[(i)*6+(j)])</span></div><div class="line"><a name="l00222"></a><span class="lineno"> 222</span> <span class="preprocessor">#define nonmpx_senscr(i) (-senscore[sseq[i]])</span></div><div class="line"><a name="l00223"></a><span class="lineno"> 223</span> </div><div class="line"><a name="l00224"></a><span class="lineno"> 224</span> <span class="keyword">static</span> int32</div><div class="line"><a name="l00225"></a><span class="lineno"> 225</span> hmm_vit_eval_5st_lr(<a class="code" href="structhmm__t.html">hmm_t</a> * hmm)</div><div class="line"><a name="l00226"></a><span class="lineno"> 226</span> {</div><div class="line"><a name="l00227"></a><span class="lineno"> 227</span>  int16 <span class="keyword">const</span> *senscore = hmm->ctx->senscore;</div><div class="line"><a name="l00228"></a><span class="lineno"> 228</span>  uint8 <span class="keyword">const</span> *tp = hmm->ctx->tp[hmm->tmatid][0];</div><div class="line"><a name="l00229"></a><span class="lineno"> 229</span>  uint16 <span class="keyword">const</span> *sseq = hmm->senid;</div><div class="line"><a name="l00230"></a><span class="lineno"> 230</span>  int32 s5, s4, s3, s2, s1, s0, t2, t1, t0, bestScore;</div><div class="line"><a name="l00231"></a><span class="lineno"> 231</span> </div><div class="line"><a name="l00232"></a><span class="lineno"> 232</span>  <span class="comment">/* It was the best of scores, it was the worst of scores. */</span></div><div class="line"><a name="l00233"></a><span class="lineno"> 233</span>  bestScore = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00234"></a><span class="lineno"> 234</span> </div><div class="line"><a name="l00235"></a><span class="lineno"> 235</span>  <span class="comment">/* Cache problem here! */</span></div><div class="line"><a name="l00236"></a><span class="lineno"> 236</span>  s4 = hmm_score(hmm, 4) + nonmpx_senscr(4);</div><div class="line"><a name="l00237"></a><span class="lineno"> 237</span>  s3 = hmm_score(hmm, 3) + nonmpx_senscr(3);</div><div class="line"><a name="l00238"></a><span class="lineno"> 238</span>  <span class="comment">/* Transitions into non-emitting state 5 */</span></div><div class="line"><a name="l00239"></a><span class="lineno"> 239</span>  <span class="keywordflow">if</span> (s3 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>) {</div><div class="line"><a name="l00240"></a><span class="lineno"> 240</span>  t1 = s4 + hmm_tprob_5st(4, 5);</div><div class="line"><a name="l00241"></a><span class="lineno"> 241</span>  t2 = s3 + hmm_tprob_5st(3, 5);</div><div class="line"><a name="l00242"></a><span class="lineno"> 242</span>  <span class="keywordflow">if</span> (t1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t2) {</div><div class="line"><a name="l00243"></a><span class="lineno"> 243</span>  s5 = t1;</div><div class="line"><a name="l00244"></a><span class="lineno"> 244</span>  hmm_out_history(hmm) = hmm_history(hmm, 4);</div><div class="line"><a name="l00245"></a><span class="lineno"> 245</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00246"></a><span class="lineno"> 246</span>  s5 = t2;</div><div class="line"><a name="l00247"></a><span class="lineno"> 247</span>  hmm_out_history(hmm) = hmm_history(hmm, 3);</div><div class="line"><a name="l00248"></a><span class="lineno"> 248</span>  }</div><div class="line"><a name="l00249"></a><span class="lineno"> 249</span>  <span class="keywordflow">if</span> (s5 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s5 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00250"></a><span class="lineno"> 250</span>  hmm_out_score(hmm) = s5;</div><div class="line"><a name="l00251"></a><span class="lineno"> 251</span>  bestScore = s5;</div><div class="line"><a name="l00252"></a><span class="lineno"> 252</span>  }</div><div class="line"><a name="l00253"></a><span class="lineno"> 253</span> </div><div class="line"><a name="l00254"></a><span class="lineno"> 254</span>  s2 = hmm_score(hmm, 2) + nonmpx_senscr(2);</div><div class="line"><a name="l00255"></a><span class="lineno"> 255</span>  <span class="comment">/* All transitions into state 4 */</span></div><div class="line"><a name="l00256"></a><span class="lineno"> 256</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> WORST_SCORE) {</div><div class="line"><a name="l00257"></a><span class="lineno"> 257</span>  t0 = s4 + hmm_tprob_5st(4, 4);</div><div class="line"><a name="l00258"></a><span class="lineno"> 258</span>  t1 = s3 + hmm_tprob_5st(3, 4);</div><div class="line"><a name="l00259"></a><span class="lineno"> 259</span>  t2 = s2 + hmm_tprob_5st(2, 4);</div><div class="line"><a name="l00260"></a><span class="lineno"> 260</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00261"></a><span class="lineno"> 261</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t0) {</div><div class="line"><a name="l00262"></a><span class="lineno"> 262</span>  s4 = t2;</div><div class="line"><a name="l00263"></a><span class="lineno"> 263</span>  hmm_history(hmm, 4) = hmm_history(hmm, 2);</div><div class="line"><a name="l00264"></a><span class="lineno"> 264</span>  } <span class="keywordflow">else</span></div><div class="line"><a name="l00265"></a><span class="lineno"> 265</span>  s4 = t0;</div><div class="line"><a name="l00266"></a><span class="lineno"> 266</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00267"></a><span class="lineno"> 267</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00268"></a><span class="lineno"> 268</span>  s4 = t2;</div><div class="line"><a name="l00269"></a><span class="lineno"> 269</span>  hmm_history(hmm, 4) = hmm_history(hmm, 2);</div><div class="line"><a name="l00270"></a><span class="lineno"> 270</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00271"></a><span class="lineno"> 271</span>  s4 = t1;</div><div class="line"><a name="l00272"></a><span class="lineno"> 272</span>  hmm_history(hmm, 4) = hmm_history(hmm, 3);</div><div class="line"><a name="l00273"></a><span class="lineno"> 273</span>  }</div><div class="line"><a name="l00274"></a><span class="lineno"> 274</span>  }</div><div class="line"><a name="l00275"></a><span class="lineno"> 275</span>  <span class="keywordflow">if</span> (s4 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s4 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00276"></a><span class="lineno"> 276</span>  <span class="keywordflow">if</span> (s4 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s4;</div><div class="line"><a name="l00277"></a><span class="lineno"> 277</span>  hmm_score(hmm, 4) = s4;</div><div class="line"><a name="l00278"></a><span class="lineno"> 278</span>  }</div><div class="line"><a name="l00279"></a><span class="lineno"> 279</span> </div><div class="line"><a name="l00280"></a><span class="lineno"> 280</span>  s1 = hmm_score(hmm, 1) + nonmpx_senscr(1);</div><div class="line"><a name="l00281"></a><span class="lineno"> 281</span>  <span class="comment">/* All transitions into state 3 */</span></div><div class="line"><a name="l00282"></a><span class="lineno"> 282</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> WORST_SCORE) {</div><div class="line"><a name="l00283"></a><span class="lineno"> 283</span>  t0 = s3 + hmm_tprob_5st(3, 3);</div><div class="line"><a name="l00284"></a><span class="lineno"> 284</span>  t1 = s2 + hmm_tprob_5st(2, 3);</div><div class="line"><a name="l00285"></a><span class="lineno"> 285</span>  t2 = s1 + hmm_tprob_5st(1, 3);</div><div class="line"><a name="l00286"></a><span class="lineno"> 286</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00287"></a><span class="lineno"> 287</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t0) {</div><div class="line"><a name="l00288"></a><span class="lineno"> 288</span>  s3 = t2;</div><div class="line"><a name="l00289"></a><span class="lineno"> 289</span>  hmm_history(hmm, 3) = hmm_history(hmm, 1);</div><div class="line"><a name="l00290"></a><span class="lineno"> 290</span>  } <span class="keywordflow">else</span></div><div class="line"><a name="l00291"></a><span class="lineno"> 291</span>  s3 = t0;</div><div class="line"><a name="l00292"></a><span class="lineno"> 292</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00293"></a><span class="lineno"> 293</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00294"></a><span class="lineno"> 294</span>  s3 = t2;</div><div class="line"><a name="l00295"></a><span class="lineno"> 295</span>  hmm_history(hmm, 3) = hmm_history(hmm, 1);</div><div class="line"><a name="l00296"></a><span class="lineno"> 296</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00297"></a><span class="lineno"> 297</span>  s3 = t1;</div><div class="line"><a name="l00298"></a><span class="lineno"> 298</span>  hmm_history(hmm, 3) = hmm_history(hmm, 2);</div><div class="line"><a name="l00299"></a><span class="lineno"> 299</span>  }</div><div class="line"><a name="l00300"></a><span class="lineno"> 300</span>  }</div><div class="line"><a name="l00301"></a><span class="lineno"> 301</span>  <span class="keywordflow">if</span> (s3 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s3 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00302"></a><span class="lineno"> 302</span>  <span class="keywordflow">if</span> (s3 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s3;</div><div class="line"><a name="l00303"></a><span class="lineno"> 303</span>  hmm_score(hmm, 3) = s3;</div><div class="line"><a name="l00304"></a><span class="lineno"> 304</span>  }</div><div class="line"><a name="l00305"></a><span class="lineno"> 305</span> </div><div class="line"><a name="l00306"></a><span class="lineno"> 306</span>  s0 = hmm_in_score(hmm) + nonmpx_senscr(0);</div><div class="line"><a name="l00307"></a><span class="lineno"> 307</span>  <span class="comment">/* All transitions into state 2 (state 0 is always active) */</span></div><div class="line"><a name="l00308"></a><span class="lineno"> 308</span>  t0 = s2 + hmm_tprob_5st(2, 2);</div><div class="line"><a name="l00309"></a><span class="lineno"> 309</span>  t1 = s1 + hmm_tprob_5st(1, 2);</div><div class="line"><a name="l00310"></a><span class="lineno"> 310</span>  t2 = s0 + hmm_tprob_5st(0, 2);</div><div class="line"><a name="l00311"></a><span class="lineno"> 311</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00312"></a><span class="lineno"> 312</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t0) {</div><div class="line"><a name="l00313"></a><span class="lineno"> 313</span>  s2 = t2;</div><div class="line"><a name="l00314"></a><span class="lineno"> 314</span>  hmm_history(hmm, 2) = hmm_in_history(hmm);</div><div class="line"><a name="l00315"></a><span class="lineno"> 315</span>  } <span class="keywordflow">else</span></div><div class="line"><a name="l00316"></a><span class="lineno"> 316</span>  s2 = t0;</div><div class="line"><a name="l00317"></a><span class="lineno"> 317</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00318"></a><span class="lineno"> 318</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00319"></a><span class="lineno"> 319</span>  s2 = t2;</div><div class="line"><a name="l00320"></a><span class="lineno"> 320</span>  hmm_history(hmm, 2) = hmm_in_history(hmm);</div><div class="line"><a name="l00321"></a><span class="lineno"> 321</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00322"></a><span class="lineno"> 322</span>  s2 = t1;</div><div class="line"><a name="l00323"></a><span class="lineno"> 323</span>  hmm_history(hmm, 2) = hmm_history(hmm, 1);</div><div class="line"><a name="l00324"></a><span class="lineno"> 324</span>  }</div><div class="line"><a name="l00325"></a><span class="lineno"> 325</span>  }</div><div class="line"><a name="l00326"></a><span class="lineno"> 326</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s2 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s2;</div><div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  hmm_score(hmm, 2) = s2;</div><div class="line"><a name="l00329"></a><span class="lineno"> 329</span> </div><div class="line"><a name="l00330"></a><span class="lineno"> 330</span> </div><div class="line"><a name="l00331"></a><span class="lineno"> 331</span>  <span class="comment">/* All transitions into state 1 */</span></div><div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  t0 = s1 + hmm_tprob_5st(1, 1);</div><div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  t1 = s0 + hmm_tprob_5st(0, 1);</div><div class="line"><a name="l00334"></a><span class="lineno"> 334</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00335"></a><span class="lineno"> 335</span>  s1 = t0;</div><div class="line"><a name="l00336"></a><span class="lineno"> 336</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  s1 = t1;</div><div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  hmm_history(hmm, 1) = hmm_in_history(hmm);</div><div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  }</div><div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s1;</div><div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  hmm_score(hmm, 1) = s1;</div><div class="line"><a name="l00343"></a><span class="lineno"> 343</span> </div><div class="line"><a name="l00344"></a><span class="lineno"> 344</span>  <span class="comment">/* All transitions into state 0 */</span></div><div class="line"><a name="l00345"></a><span class="lineno"> 345</span>  s0 = s0 + hmm_tprob_5st(0, 0);</div><div class="line"><a name="l00346"></a><span class="lineno"> 346</span>  <span class="keywordflow">if</span> (s0 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s0 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00347"></a><span class="lineno"> 347</span>  <span class="keywordflow">if</span> (s0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s0;</div><div class="line"><a name="l00348"></a><span class="lineno"> 348</span>  hmm_in_score(hmm) = s0;</div><div class="line"><a name="l00349"></a><span class="lineno"> 349</span> </div><div class="line"><a name="l00350"></a><span class="lineno"> 350</span>  hmm_bestscore(hmm) = bestScore;</div><div class="line"><a name="l00351"></a><span class="lineno"> 351</span>  <span class="keywordflow">return</span> bestScore;</div><div class="line"><a name="l00352"></a><span class="lineno"> 352</span> }</div><div class="line"><a name="l00353"></a><span class="lineno"> 353</span> </div><div class="line"><a name="l00354"></a><span class="lineno"> 354</span> <span class="preprocessor">#define mpx_senid(st) sseq[ssid[st]][st]</span></div><div class="line"><a name="l00355"></a><span class="lineno"> 355</span> <span class="preprocessor">#define mpx_senscr(st) (-senscore[mpx_senid(st)])</span></div><div class="line"><a name="l00356"></a><span class="lineno"> 356</span> </div><div class="line"><a name="l00357"></a><span class="lineno"> 357</span> <span class="keyword">static</span> int32</div><div class="line"><a name="l00358"></a><span class="lineno"> 358</span> hmm_vit_eval_5st_lr_mpx(<a class="code" href="structhmm__t.html">hmm_t</a> * hmm)</div><div class="line"><a name="l00359"></a><span class="lineno"> 359</span> {</div><div class="line"><a name="l00360"></a><span class="lineno"> 360</span>  uint8 <span class="keyword">const</span> *tp = hmm->ctx->tp[hmm->tmatid][0];</div><div class="line"><a name="l00361"></a><span class="lineno"> 361</span>  int16 <span class="keyword">const</span> *senscore = hmm->ctx->senscore;</div><div class="line"><a name="l00362"></a><span class="lineno"> 362</span>  uint16 * <span class="keyword">const</span> *sseq = hmm->ctx->sseq;</div><div class="line"><a name="l00363"></a><span class="lineno"> 363</span>  uint16 *ssid = hmm->senid;</div><div class="line"><a name="l00364"></a><span class="lineno"> 364</span>  int32 bestScore;</div><div class="line"><a name="l00365"></a><span class="lineno"> 365</span>  int32 s5, s4, s3, s2, s1, s0, t2, t1, t0;</div><div class="line"><a name="l00366"></a><span class="lineno"> 366</span> </div><div class="line"><a name="l00367"></a><span class="lineno"> 367</span>  <span class="comment">/* Don't propagate WORST_SCORE */</span></div><div class="line"><a name="l00368"></a><span class="lineno"> 368</span>  <span class="keywordflow">if</span> (ssid[4] == <a class="code" href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a>)</div><div class="line"><a name="l00369"></a><span class="lineno"> 369</span>  s4 = t1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00370"></a><span class="lineno"> 370</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00371"></a><span class="lineno"> 371</span>  s4 = hmm_score(hmm, 4) + mpx_senscr(4);</div><div class="line"><a name="l00372"></a><span class="lineno"> 372</span>  t1 = s4 + hmm_tprob_5st(4, 5);</div><div class="line"><a name="l00373"></a><span class="lineno"> 373</span>  }</div><div class="line"><a name="l00374"></a><span class="lineno"> 374</span>  <span class="keywordflow">if</span> (ssid[3] == <a class="code" href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a>)</div><div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  s3 = t2 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00376"></a><span class="lineno"> 376</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00377"></a><span class="lineno"> 377</span>  s3 = hmm_score(hmm, 3) + mpx_senscr(3);</div><div class="line"><a name="l00378"></a><span class="lineno"> 378</span>  t2 = s3 + hmm_tprob_5st(3, 5);</div><div class="line"><a name="l00379"></a><span class="lineno"> 379</span>  }</div><div class="line"><a name="l00380"></a><span class="lineno"> 380</span>  <span class="keywordflow">if</span> (t1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t2) {</div><div class="line"><a name="l00381"></a><span class="lineno"> 381</span>  s5 = t1;</div><div class="line"><a name="l00382"></a><span class="lineno"> 382</span>  hmm_out_history(hmm) = hmm_history(hmm, 4);</div><div class="line"><a name="l00383"></a><span class="lineno"> 383</span>  }</div><div class="line"><a name="l00384"></a><span class="lineno"> 384</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00385"></a><span class="lineno"> 385</span>  s5 = t2;</div><div class="line"><a name="l00386"></a><span class="lineno"> 386</span>  hmm_out_history(hmm) = hmm_history(hmm, 3);</div><div class="line"><a name="l00387"></a><span class="lineno"> 387</span>  }</div><div class="line"><a name="l00388"></a><span class="lineno"> 388</span>  <span class="keywordflow">if</span> (s5 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>) s5 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00389"></a><span class="lineno"> 389</span>  hmm_out_score(hmm) = s5;</div><div class="line"><a name="l00390"></a><span class="lineno"> 390</span>  bestScore = s5;</div><div class="line"><a name="l00391"></a><span class="lineno"> 391</span> </div><div class="line"><a name="l00392"></a><span class="lineno"> 392</span>  <span class="comment">/* Don't propagate WORST_SCORE */</span></div><div class="line"><a name="l00393"></a><span class="lineno"> 393</span>  <span class="keywordflow">if</span> (ssid[2] == <a class="code" href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a>)</div><div class="line"><a name="l00394"></a><span class="lineno"> 394</span>  s2 = t2 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00396"></a><span class="lineno"> 396</span>  s2 = hmm_score(hmm, 2) + mpx_senscr(2);</div><div class="line"><a name="l00397"></a><span class="lineno"> 397</span>  t2 = s2 + hmm_tprob_5st(2, 4);</div><div class="line"><a name="l00398"></a><span class="lineno"> 398</span>  }</div><div class="line"><a name="l00399"></a><span class="lineno"> 399</span> </div><div class="line"><a name="l00400"></a><span class="lineno"> 400</span>  t0 = t1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00401"></a><span class="lineno"> 401</span>  <span class="keywordflow">if</span> (s4 != WORST_SCORE)</div><div class="line"><a name="l00402"></a><span class="lineno"> 402</span>  t0 = s4 + hmm_tprob_5st(4, 4);</div><div class="line"><a name="l00403"></a><span class="lineno"> 403</span>  <span class="keywordflow">if</span> (s3 != WORST_SCORE)</div><div class="line"><a name="l00404"></a><span class="lineno"> 404</span>  t1 = s3 + hmm_tprob_5st(3, 4);</div><div class="line"><a name="l00405"></a><span class="lineno"> 405</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00406"></a><span class="lineno"> 406</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t0) {</div><div class="line"><a name="l00407"></a><span class="lineno"> 407</span>  s4 = t2;</div><div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  hmm_history(hmm, 4) = hmm_history(hmm, 2);</div><div class="line"><a name="l00409"></a><span class="lineno"> 409</span>  ssid[4] = ssid[2];</div><div class="line"><a name="l00410"></a><span class="lineno"> 410</span>  }</div><div class="line"><a name="l00411"></a><span class="lineno"> 411</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00412"></a><span class="lineno"> 412</span>  s4 = t0;</div><div class="line"><a name="l00413"></a><span class="lineno"> 413</span>  }</div><div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00415"></a><span class="lineno"> 415</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00416"></a><span class="lineno"> 416</span>  s4 = t2;</div><div class="line"><a name="l00417"></a><span class="lineno"> 417</span>  hmm_history(hmm, 4) = hmm_history(hmm, 2);</div><div class="line"><a name="l00418"></a><span class="lineno"> 418</span>  ssid[4] = ssid[2];</div><div class="line"><a name="l00419"></a><span class="lineno"> 419</span>  }</div><div class="line"><a name="l00420"></a><span class="lineno"> 420</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00421"></a><span class="lineno"> 421</span>  s4 = t1;</div><div class="line"><a name="l00422"></a><span class="lineno"> 422</span>  hmm_history(hmm, 4) = hmm_history(hmm, 3);</div><div class="line"><a name="l00423"></a><span class="lineno"> 423</span>  ssid[4] = ssid[3];</div><div class="line"><a name="l00424"></a><span class="lineno"> 424</span>  }</div><div class="line"><a name="l00425"></a><span class="lineno"> 425</span>  }</div><div class="line"><a name="l00426"></a><span class="lineno"> 426</span>  <span class="keywordflow">if</span> (s4 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s4 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00427"></a><span class="lineno"> 427</span>  <span class="keywordflow">if</span> (s4 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore)</div><div class="line"><a name="l00428"></a><span class="lineno"> 428</span>  bestScore = s4;</div><div class="line"><a name="l00429"></a><span class="lineno"> 429</span>  hmm_score(hmm, 4) = s4;</div><div class="line"><a name="l00430"></a><span class="lineno"> 430</span> </div><div class="line"><a name="l00431"></a><span class="lineno"> 431</span>  <span class="comment">/* Don't propagate WORST_SCORE */</span></div><div class="line"><a name="l00432"></a><span class="lineno"> 432</span>  <span class="keywordflow">if</span> (ssid[1] == <a class="code" href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a>)</div><div class="line"><a name="l00433"></a><span class="lineno"> 433</span>  s1 = t2 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00434"></a><span class="lineno"> 434</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00435"></a><span class="lineno"> 435</span>  s1 = hmm_score(hmm, 1) + mpx_senscr(1);</div><div class="line"><a name="l00436"></a><span class="lineno"> 436</span>  t2 = s1 + hmm_tprob_5st(1, 3);</div><div class="line"><a name="l00437"></a><span class="lineno"> 437</span>  }</div><div class="line"><a name="l00438"></a><span class="lineno"> 438</span>  t0 = t1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00439"></a><span class="lineno"> 439</span>  <span class="keywordflow">if</span> (s3 != WORST_SCORE)</div><div class="line"><a name="l00440"></a><span class="lineno"> 440</span>  t0 = s3 + hmm_tprob_5st(3, 3);</div><div class="line"><a name="l00441"></a><span class="lineno"> 441</span>  <span class="keywordflow">if</span> (s2 != WORST_SCORE)</div><div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  t1 = s2 + hmm_tprob_5st(2, 3);</div><div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00444"></a><span class="lineno"> 444</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t0) {</div><div class="line"><a name="l00445"></a><span class="lineno"> 445</span>  s3 = t2;</div><div class="line"><a name="l00446"></a><span class="lineno"> 446</span>  hmm_history(hmm, 3) = hmm_history(hmm, 1);</div><div class="line"><a name="l00447"></a><span class="lineno"> 447</span>  ssid[3] = ssid[1];</div><div class="line"><a name="l00448"></a><span class="lineno"> 448</span>  }</div><div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  s3 = t0;</div><div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  }</div><div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00454"></a><span class="lineno"> 454</span>  s3 = t2;</div><div class="line"><a name="l00455"></a><span class="lineno"> 455</span>  hmm_history(hmm, 3) = hmm_history(hmm, 1);</div><div class="line"><a name="l00456"></a><span class="lineno"> 456</span>  ssid[3] = ssid[1];</div><div class="line"><a name="l00457"></a><span class="lineno"> 457</span>  }</div><div class="line"><a name="l00458"></a><span class="lineno"> 458</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  s3 = t1;</div><div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  hmm_history(hmm, 3) = hmm_history(hmm, 2);</div><div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  ssid[3] = ssid[2];</div><div class="line"><a name="l00462"></a><span class="lineno"> 462</span>  }</div><div class="line"><a name="l00463"></a><span class="lineno"> 463</span>  }</div><div class="line"><a name="l00464"></a><span class="lineno"> 464</span>  <span class="keywordflow">if</span> (s3 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s3 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00465"></a><span class="lineno"> 465</span>  <span class="keywordflow">if</span> (s3 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s3;</div><div class="line"><a name="l00466"></a><span class="lineno"> 466</span>  hmm_score(hmm, 3) = s3;</div><div class="line"><a name="l00467"></a><span class="lineno"> 467</span> </div><div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  <span class="comment">/* State 0 is always active */</span></div><div class="line"><a name="l00469"></a><span class="lineno"> 469</span>  s0 = hmm_in_score(hmm) + mpx_senscr(0);</div><div class="line"><a name="l00470"></a><span class="lineno"> 470</span> </div><div class="line"><a name="l00471"></a><span class="lineno"> 471</span>  <span class="comment">/* Don't propagate WORST_SCORE */</span></div><div class="line"><a name="l00472"></a><span class="lineno"> 472</span>  t0 = t1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00473"></a><span class="lineno"> 473</span>  <span class="keywordflow">if</span> (s2 != WORST_SCORE)</div><div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  t0 = s2 + hmm_tprob_5st(2, 2);</div><div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  <span class="keywordflow">if</span> (s1 != WORST_SCORE)</div><div class="line"><a name="l00476"></a><span class="lineno"> 476</span>  t1 = s1 + hmm_tprob_5st(1, 2);</div><div class="line"><a name="l00477"></a><span class="lineno"> 477</span>  t2 = s0 + hmm_tprob_5st(0, 2);</div><div class="line"><a name="l00478"></a><span class="lineno"> 478</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00479"></a><span class="lineno"> 479</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t0) {</div><div class="line"><a name="l00480"></a><span class="lineno"> 480</span>  s2 = t2;</div><div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  hmm_history(hmm, 2) = hmm_in_history(hmm);</div><div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  ssid[2] = ssid[0];</div><div class="line"><a name="l00483"></a><span class="lineno"> 483</span>  }</div><div class="line"><a name="l00484"></a><span class="lineno"> 484</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00485"></a><span class="lineno"> 485</span>  s2 = t0;</div><div class="line"><a name="l00486"></a><span class="lineno"> 486</span>  }</div><div class="line"><a name="l00487"></a><span class="lineno"> 487</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00488"></a><span class="lineno"> 488</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00489"></a><span class="lineno"> 489</span>  s2 = t2;</div><div class="line"><a name="l00490"></a><span class="lineno"> 490</span>  hmm_history(hmm, 2) = hmm_in_history(hmm);</div><div class="line"><a name="l00491"></a><span class="lineno"> 491</span>  ssid[2] = ssid[0];</div><div class="line"><a name="l00492"></a><span class="lineno"> 492</span>  }</div><div class="line"><a name="l00493"></a><span class="lineno"> 493</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00494"></a><span class="lineno"> 494</span>  s2 = t1;</div><div class="line"><a name="l00495"></a><span class="lineno"> 495</span>  hmm_history(hmm, 2) = hmm_history(hmm, 1);</div><div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  ssid[2] = ssid[1];</div><div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  }</div><div class="line"><a name="l00498"></a><span class="lineno"> 498</span>  }</div><div class="line"><a name="l00499"></a><span class="lineno"> 499</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s2 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00500"></a><span class="lineno"> 500</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s2;</div><div class="line"><a name="l00501"></a><span class="lineno"> 501</span>  hmm_score(hmm, 2) = s2;</div><div class="line"><a name="l00502"></a><span class="lineno"> 502</span> </div><div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="comment">/* Don't propagate WORST_SCORE */</span></div><div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  t0 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00505"></a><span class="lineno"> 505</span>  <span class="keywordflow">if</span> (s1 != WORST_SCORE)</div><div class="line"><a name="l00506"></a><span class="lineno"> 506</span>  t0 = s1 + hmm_tprob_5st(1, 1);</div><div class="line"><a name="l00507"></a><span class="lineno"> 507</span>  t1 = s0 + hmm_tprob_5st(0, 1);</div><div class="line"><a name="l00508"></a><span class="lineno"> 508</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00509"></a><span class="lineno"> 509</span>  s1 = t0;</div><div class="line"><a name="l00510"></a><span class="lineno"> 510</span>  }</div><div class="line"><a name="l00511"></a><span class="lineno"> 511</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00512"></a><span class="lineno"> 512</span>  s1 = t1;</div><div class="line"><a name="l00513"></a><span class="lineno"> 513</span>  hmm_history(hmm, 1) = hmm_in_history(hmm);</div><div class="line"><a name="l00514"></a><span class="lineno"> 514</span>  ssid[1] = ssid[0];</div><div class="line"><a name="l00515"></a><span class="lineno"> 515</span>  }</div><div class="line"><a name="l00516"></a><span class="lineno"> 516</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00517"></a><span class="lineno"> 517</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s1;</div><div class="line"><a name="l00518"></a><span class="lineno"> 518</span>  hmm_score(hmm, 1) = s1;</div><div class="line"><a name="l00519"></a><span class="lineno"> 519</span> </div><div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  s0 += hmm_tprob_5st(0, 0);</div><div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  <span class="keywordflow">if</span> (s0 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s0 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00522"></a><span class="lineno"> 522</span>  <span class="keywordflow">if</span> (s0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s0;</div><div class="line"><a name="l00523"></a><span class="lineno"> 523</span>  hmm_in_score(hmm) = s0;</div><div class="line"><a name="l00524"></a><span class="lineno"> 524</span> </div><div class="line"><a name="l00525"></a><span class="lineno"> 525</span>  hmm_bestscore(hmm) = bestScore;</div><div class="line"><a name="l00526"></a><span class="lineno"> 526</span>  <span class="keywordflow">return</span> bestScore;</div><div class="line"><a name="l00527"></a><span class="lineno"> 527</span> }</div><div class="line"><a name="l00528"></a><span class="lineno"> 528</span> </div><div class="line"><a name="l00529"></a><span class="lineno"> 529</span> <span class="preprocessor">#define hmm_tprob_3st(i, j) (-tp[(i)*4+(j)])</span></div><div class="line"><a name="l00530"></a><span class="lineno"> 530</span> </div><div class="line"><a name="l00531"></a><span class="lineno"> 531</span> <span class="keyword">static</span> int32</div><div class="line"><a name="l00532"></a><span class="lineno"> 532</span> hmm_vit_eval_3st_lr(<a class="code" href="structhmm__t.html">hmm_t</a> * hmm)</div><div class="line"><a name="l00533"></a><span class="lineno"> 533</span> {</div><div class="line"><a name="l00534"></a><span class="lineno"> 534</span>  int16 <span class="keyword">const</span> *senscore = hmm->ctx->senscore;</div><div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  uint8 <span class="keyword">const</span> *tp = hmm->ctx->tp[hmm->tmatid][0];</div><div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  uint16 <span class="keyword">const</span> *sseq = hmm->senid;</div><div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  int32 s3, s2, s1, s0, t2, t1, t0, bestScore;</div><div class="line"><a name="l00538"></a><span class="lineno"> 538</span> </div><div class="line"><a name="l00539"></a><span class="lineno"> 539</span>  s2 = hmm_score(hmm, 2) + nonmpx_senscr(2);</div><div class="line"><a name="l00540"></a><span class="lineno"> 540</span>  s1 = hmm_score(hmm, 1) + nonmpx_senscr(1);</div><div class="line"><a name="l00541"></a><span class="lineno"> 541</span>  s0 = hmm_in_score(hmm) + nonmpx_senscr(0);</div><div class="line"><a name="l00542"></a><span class="lineno"> 542</span> </div><div class="line"><a name="l00543"></a><span class="lineno"> 543</span>  <span class="comment">/* It was the best of scores, it was the worst of scores. */</span></div><div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  bestScore = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  t2 = INT_MIN; <span class="comment">/* Not used unless skipstate is true */</span></div><div class="line"><a name="l00546"></a><span class="lineno"> 546</span> </div><div class="line"><a name="l00547"></a><span class="lineno"> 547</span>  <span class="comment">/* Transitions into non-emitting state 3 */</span></div><div class="line"><a name="l00548"></a><span class="lineno"> 548</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>) {</div><div class="line"><a name="l00549"></a><span class="lineno"> 549</span>  t1 = s2 + hmm_tprob_3st(2, 3);</div><div class="line"><a name="l00550"></a><span class="lineno"> 550</span>  <span class="keywordflow">if</span> (hmm_tprob_3st(1,3) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a9b38399b544dbb93bc9b7d0094e91db7">TMAT_WORST_SCORE</a>)</div><div class="line"><a name="l00551"></a><span class="lineno"> 551</span>  t2 = s1 + hmm_tprob_3st(1, 3);</div><div class="line"><a name="l00552"></a><span class="lineno"> 552</span>  <span class="keywordflow">if</span> (t1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t2) {</div><div class="line"><a name="l00553"></a><span class="lineno"> 553</span>  s3 = t1;</div><div class="line"><a name="l00554"></a><span class="lineno"> 554</span>  hmm_out_history(hmm) = hmm_history(hmm, 2);</div><div class="line"><a name="l00555"></a><span class="lineno"> 555</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  s3 = t2;</div><div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  hmm_out_history(hmm) = hmm_history(hmm, 1);</div><div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  }</div><div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  <span class="keywordflow">if</span> (s3 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s3 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00560"></a><span class="lineno"> 560</span>  hmm_out_score(hmm) = s3;</div><div class="line"><a name="l00561"></a><span class="lineno"> 561</span>  bestScore = s3;</div><div class="line"><a name="l00562"></a><span class="lineno"> 562</span>  }</div><div class="line"><a name="l00563"></a><span class="lineno"> 563</span> </div><div class="line"><a name="l00564"></a><span class="lineno"> 564</span>  <span class="comment">/* All transitions into state 2 (state 0 is always active) */</span></div><div class="line"><a name="l00565"></a><span class="lineno"> 565</span>  t0 = s2 + hmm_tprob_3st(2, 2);</div><div class="line"><a name="l00566"></a><span class="lineno"> 566</span>  t1 = s1 + hmm_tprob_3st(1, 2);</div><div class="line"><a name="l00567"></a><span class="lineno"> 567</span>  <span class="keywordflow">if</span> (hmm_tprob_3st(0, 2) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a9b38399b544dbb93bc9b7d0094e91db7">TMAT_WORST_SCORE</a>)</div><div class="line"><a name="l00568"></a><span class="lineno"> 568</span>  t2 = s0 + hmm_tprob_3st(0, 2);</div><div class="line"><a name="l00569"></a><span class="lineno"> 569</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00570"></a><span class="lineno"> 570</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t0) {</div><div class="line"><a name="l00571"></a><span class="lineno"> 571</span>  s2 = t2;</div><div class="line"><a name="l00572"></a><span class="lineno"> 572</span>  hmm_history(hmm, 2) = hmm_in_history(hmm);</div><div class="line"><a name="l00573"></a><span class="lineno"> 573</span>  } <span class="keywordflow">else</span></div><div class="line"><a name="l00574"></a><span class="lineno"> 574</span>  s2 = t0;</div><div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00576"></a><span class="lineno"> 576</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00577"></a><span class="lineno"> 577</span>  s2 = t2;</div><div class="line"><a name="l00578"></a><span class="lineno"> 578</span>  hmm_history(hmm, 2) = hmm_in_history(hmm);</div><div class="line"><a name="l00579"></a><span class="lineno"> 579</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00580"></a><span class="lineno"> 580</span>  s2 = t1;</div><div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  hmm_history(hmm, 2) = hmm_history(hmm, 1);</div><div class="line"><a name="l00582"></a><span class="lineno"> 582</span>  }</div><div class="line"><a name="l00583"></a><span class="lineno"> 583</span>  }</div><div class="line"><a name="l00584"></a><span class="lineno"> 584</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s2 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00585"></a><span class="lineno"> 585</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s2;</div><div class="line"><a name="l00586"></a><span class="lineno"> 586</span>  hmm_score(hmm, 2) = s2;</div><div class="line"><a name="l00587"></a><span class="lineno"> 587</span> </div><div class="line"><a name="l00588"></a><span class="lineno"> 588</span>  <span class="comment">/* All transitions into state 1 */</span></div><div class="line"><a name="l00589"></a><span class="lineno"> 589</span>  t0 = s1 + hmm_tprob_3st(1, 1);</div><div class="line"><a name="l00590"></a><span class="lineno"> 590</span>  t1 = s0 + hmm_tprob_3st(0, 1);</div><div class="line"><a name="l00591"></a><span class="lineno"> 591</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00592"></a><span class="lineno"> 592</span>  s1 = t0;</div><div class="line"><a name="l00593"></a><span class="lineno"> 593</span>  } <span class="keywordflow">else</span> {</div><div class="line"><a name="l00594"></a><span class="lineno"> 594</span>  s1 = t1;</div><div class="line"><a name="l00595"></a><span class="lineno"> 595</span>  hmm_history(hmm, 1) = hmm_in_history(hmm);</div><div class="line"><a name="l00596"></a><span class="lineno"> 596</span>  }</div><div class="line"><a name="l00597"></a><span class="lineno"> 597</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00598"></a><span class="lineno"> 598</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s1;</div><div class="line"><a name="l00599"></a><span class="lineno"> 599</span>  hmm_score(hmm, 1) = s1;</div><div class="line"><a name="l00600"></a><span class="lineno"> 600</span> </div><div class="line"><a name="l00601"></a><span class="lineno"> 601</span>  <span class="comment">/* All transitions into state 0 */</span></div><div class="line"><a name="l00602"></a><span class="lineno"> 602</span>  s0 = s0 + hmm_tprob_3st(0, 0);</div><div class="line"><a name="l00603"></a><span class="lineno"> 603</span>  <span class="keywordflow">if</span> (s0 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s0 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00604"></a><span class="lineno"> 604</span>  <span class="keywordflow">if</span> (s0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s0;</div><div class="line"><a name="l00605"></a><span class="lineno"> 605</span>  hmm_in_score(hmm) = s0;</div><div class="line"><a name="l00606"></a><span class="lineno"> 606</span> </div><div class="line"><a name="l00607"></a><span class="lineno"> 607</span>  hmm_bestscore(hmm) = bestScore;</div><div class="line"><a name="l00608"></a><span class="lineno"> 608</span>  <span class="keywordflow">return</span> bestScore;</div><div class="line"><a name="l00609"></a><span class="lineno"> 609</span> }</div><div class="line"><a name="l00610"></a><span class="lineno"> 610</span> </div><div class="line"><a name="l00611"></a><span class="lineno"> 611</span> <span class="keyword">static</span> int32</div><div class="line"><a name="l00612"></a><span class="lineno"> 612</span> hmm_vit_eval_3st_lr_mpx(<a class="code" href="structhmm__t.html">hmm_t</a> * hmm)</div><div class="line"><a name="l00613"></a><span class="lineno"> 613</span> {</div><div class="line"><a name="l00614"></a><span class="lineno"> 614</span>  uint8 <span class="keyword">const</span> *tp = hmm->ctx->tp[hmm->tmatid][0];</div><div class="line"><a name="l00615"></a><span class="lineno"> 615</span>  int16 <span class="keyword">const</span> *senscore = hmm->ctx->senscore;</div><div class="line"><a name="l00616"></a><span class="lineno"> 616</span>  uint16 * <span class="keyword">const</span> *sseq = hmm->ctx->sseq;</div><div class="line"><a name="l00617"></a><span class="lineno"> 617</span>  uint16 *ssid = hmm->senid;</div><div class="line"><a name="l00618"></a><span class="lineno"> 618</span>  int32 bestScore;</div><div class="line"><a name="l00619"></a><span class="lineno"> 619</span>  int32 s3, s2, s1, s0, t2, t1, t0;</div><div class="line"><a name="l00620"></a><span class="lineno"> 620</span> </div><div class="line"><a name="l00621"></a><span class="lineno"> 621</span>  <span class="comment">/* Don't propagate WORST_SCORE */</span></div><div class="line"><a name="l00622"></a><span class="lineno"> 622</span>  t2 = INT_MIN; <span class="comment">/* Not used unless skipstate is true */</span></div><div class="line"><a name="l00623"></a><span class="lineno"> 623</span>  <span class="keywordflow">if</span> (ssid[2] == <a class="code" href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a>)</div><div class="line"><a name="l00624"></a><span class="lineno"> 624</span>  s2 = t1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00625"></a><span class="lineno"> 625</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00626"></a><span class="lineno"> 626</span>  s2 = hmm_score(hmm, 2) + mpx_senscr(2);</div><div class="line"><a name="l00627"></a><span class="lineno"> 627</span>  t1 = s2 + hmm_tprob_3st(2, 3);</div><div class="line"><a name="l00628"></a><span class="lineno"> 628</span>  }</div><div class="line"><a name="l00629"></a><span class="lineno"> 629</span>  <span class="keywordflow">if</span> (ssid[1] == <a class="code" href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a>)</div><div class="line"><a name="l00630"></a><span class="lineno"> 630</span>  s1 = t2 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00631"></a><span class="lineno"> 631</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00632"></a><span class="lineno"> 632</span>  s1 = hmm_score(hmm, 1) + mpx_senscr(1);</div><div class="line"><a name="l00633"></a><span class="lineno"> 633</span>  <span class="keywordflow">if</span> (hmm_tprob_3st(1,3) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a9b38399b544dbb93bc9b7d0094e91db7">TMAT_WORST_SCORE</a>)</div><div class="line"><a name="l00634"></a><span class="lineno"> 634</span>  t2 = s1 + hmm_tprob_3st(1, 3);</div><div class="line"><a name="l00635"></a><span class="lineno"> 635</span>  }</div><div class="line"><a name="l00636"></a><span class="lineno"> 636</span>  <span class="keywordflow">if</span> (t1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t2) {</div><div class="line"><a name="l00637"></a><span class="lineno"> 637</span>  s3 = t1;</div><div class="line"><a name="l00638"></a><span class="lineno"> 638</span>  hmm_out_history(hmm) = hmm_history(hmm, 2);</div><div class="line"><a name="l00639"></a><span class="lineno"> 639</span>  }</div><div class="line"><a name="l00640"></a><span class="lineno"> 640</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00641"></a><span class="lineno"> 641</span>  s3 = t2;</div><div class="line"><a name="l00642"></a><span class="lineno"> 642</span>  hmm_out_history(hmm) = hmm_history(hmm, 1);</div><div class="line"><a name="l00643"></a><span class="lineno"> 643</span>  }</div><div class="line"><a name="l00644"></a><span class="lineno"> 644</span>  <span class="keywordflow">if</span> (s3 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>) s3 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00645"></a><span class="lineno"> 645</span>  hmm_out_score(hmm) = s3;</div><div class="line"><a name="l00646"></a><span class="lineno"> 646</span>  bestScore = s3;</div><div class="line"><a name="l00647"></a><span class="lineno"> 647</span> </div><div class="line"><a name="l00648"></a><span class="lineno"> 648</span>  <span class="comment">/* State 0 is always active */</span></div><div class="line"><a name="l00649"></a><span class="lineno"> 649</span>  s0 = hmm_in_score(hmm) + mpx_senscr(0);</div><div class="line"><a name="l00650"></a><span class="lineno"> 650</span> </div><div class="line"><a name="l00651"></a><span class="lineno"> 651</span>  <span class="comment">/* Don't propagate WORST_SCORE */</span></div><div class="line"><a name="l00652"></a><span class="lineno"> 652</span>  t0 = t1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00653"></a><span class="lineno"> 653</span>  <span class="keywordflow">if</span> (s2 != WORST_SCORE)</div><div class="line"><a name="l00654"></a><span class="lineno"> 654</span>  t0 = s2 + hmm_tprob_3st(2, 2);</div><div class="line"><a name="l00655"></a><span class="lineno"> 655</span>  <span class="keywordflow">if</span> (s1 != WORST_SCORE)</div><div class="line"><a name="l00656"></a><span class="lineno"> 656</span>  t1 = s1 + hmm_tprob_3st(1, 2);</div><div class="line"><a name="l00657"></a><span class="lineno"> 657</span>  <span class="keywordflow">if</span> (hmm_tprob_3st(0,2) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a9b38399b544dbb93bc9b7d0094e91db7">TMAT_WORST_SCORE</a>)</div><div class="line"><a name="l00658"></a><span class="lineno"> 658</span>  t2 = s0 + hmm_tprob_3st(0, 2);</div><div class="line"><a name="l00659"></a><span class="lineno"> 659</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t0) {</div><div class="line"><a name="l00661"></a><span class="lineno"> 661</span>  s2 = t2;</div><div class="line"><a name="l00662"></a><span class="lineno"> 662</span>  hmm_history(hmm, 2) = hmm_in_history(hmm);</div><div class="line"><a name="l00663"></a><span class="lineno"> 663</span>  ssid[2] = ssid[0];</div><div class="line"><a name="l00664"></a><span class="lineno"> 664</span>  }</div><div class="line"><a name="l00665"></a><span class="lineno"> 665</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00666"></a><span class="lineno"> 666</span>  s2 = t0;</div><div class="line"><a name="l00667"></a><span class="lineno"> 667</span>  }</div><div class="line"><a name="l00668"></a><span class="lineno"> 668</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00669"></a><span class="lineno"> 669</span>  <span class="keywordflow">if</span> (t2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00670"></a><span class="lineno"> 670</span>  s2 = t2;</div><div class="line"><a name="l00671"></a><span class="lineno"> 671</span>  hmm_history(hmm, 2) = hmm_in_history(hmm);</div><div class="line"><a name="l00672"></a><span class="lineno"> 672</span>  ssid[2] = ssid[0];</div><div class="line"><a name="l00673"></a><span class="lineno"> 673</span>  }</div><div class="line"><a name="l00674"></a><span class="lineno"> 674</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00675"></a><span class="lineno"> 675</span>  s2 = t1;</div><div class="line"><a name="l00676"></a><span class="lineno"> 676</span>  hmm_history(hmm, 2) = hmm_history(hmm, 1);</div><div class="line"><a name="l00677"></a><span class="lineno"> 677</span>  ssid[2] = ssid[1];</div><div class="line"><a name="l00678"></a><span class="lineno"> 678</span>  }</div><div class="line"><a name="l00679"></a><span class="lineno"> 679</span>  }</div><div class="line"><a name="l00680"></a><span class="lineno"> 680</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s2 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00681"></a><span class="lineno"> 681</span>  <span class="keywordflow">if</span> (s2 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s2;</div><div class="line"><a name="l00682"></a><span class="lineno"> 682</span>  hmm_score(hmm, 2) = s2;</div><div class="line"><a name="l00683"></a><span class="lineno"> 683</span> </div><div class="line"><a name="l00684"></a><span class="lineno"> 684</span>  <span class="comment">/* Don't propagate WORST_SCORE */</span></div><div class="line"><a name="l00685"></a><span class="lineno"> 685</span>  t0 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00686"></a><span class="lineno"> 686</span>  <span class="keywordflow">if</span> (s1 != WORST_SCORE)</div><div class="line"><a name="l00687"></a><span class="lineno"> 687</span>  t0 = s1 + hmm_tprob_3st(1, 1);</div><div class="line"><a name="l00688"></a><span class="lineno"> 688</span>  t1 = s0 + hmm_tprob_3st(0, 1);</div><div class="line"><a name="l00689"></a><span class="lineno"> 689</span>  <span class="keywordflow">if</span> (t0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> t1) {</div><div class="line"><a name="l00690"></a><span class="lineno"> 690</span>  s1 = t0;</div><div class="line"><a name="l00691"></a><span class="lineno"> 691</span>  }</div><div class="line"><a name="l00692"></a><span class="lineno"> 692</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00693"></a><span class="lineno"> 693</span>  s1 = t1;</div><div class="line"><a name="l00694"></a><span class="lineno"> 694</span>  hmm_history(hmm, 1) = hmm_in_history(hmm);</div><div class="line"><a name="l00695"></a><span class="lineno"> 695</span>  ssid[1] = ssid[0];</div><div class="line"><a name="l00696"></a><span class="lineno"> 696</span>  }</div><div class="line"><a name="l00697"></a><span class="lineno"> 697</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s1 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00698"></a><span class="lineno"> 698</span>  <span class="keywordflow">if</span> (s1 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s1;</div><div class="line"><a name="l00699"></a><span class="lineno"> 699</span>  hmm_score(hmm, 1) = s1;</div><div class="line"><a name="l00700"></a><span class="lineno"> 700</span> </div><div class="line"><a name="l00701"></a><span class="lineno"> 701</span>  <span class="comment">/* State 0 is always active */</span></div><div class="line"><a name="l00702"></a><span class="lineno"> 702</span>  s0 += hmm_tprob_3st(0, 0);</div><div class="line"><a name="l00703"></a><span class="lineno"> 703</span>  <span class="keywordflow">if</span> (s0 <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> WORST_SCORE) s0 = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00704"></a><span class="lineno"> 704</span>  <span class="keywordflow">if</span> (s0 <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> bestScore) bestScore = s0;</div><div class="line"><a name="l00705"></a><span class="lineno"> 705</span>  hmm_in_score(hmm) = s0;</div><div class="line"><a name="l00706"></a><span class="lineno"> 706</span> </div><div class="line"><a name="l00707"></a><span class="lineno"> 707</span>  hmm_bestscore(hmm) = bestScore;</div><div class="line"><a name="l00708"></a><span class="lineno"> 708</span>  <span class="keywordflow">return</span> bestScore;</div><div class="line"><a name="l00709"></a><span class="lineno"> 709</span> }</div><div class="line"><a name="l00710"></a><span class="lineno"> 710</span> </div><div class="line"><a name="l00711"></a><span class="lineno"> 711</span> <span class="keyword">static</span> int32</div><div class="line"><a name="l00712"></a><span class="lineno"> 712</span> hmm_vit_eval_anytopo(<a class="code" href="structhmm__t.html">hmm_t</a> * hmm)</div><div class="line"><a name="l00713"></a><span class="lineno"> 713</span> {</div><div class="line"><a name="l00714"></a><span class="lineno"> 714</span>  <a class="code" href="structhmm__context__t.html">hmm_context_t</a> *ctx = hmm->ctx;</div><div class="line"><a name="l00715"></a><span class="lineno"> 715</span>  int32 to, from, bestfrom;</div><div class="line"><a name="l00716"></a><span class="lineno"> 716</span>  int32 newscr, scr, bestscr;</div><div class="line"><a name="l00717"></a><span class="lineno"> 717</span>  <span class="keywordtype">int</span> final_state;</div><div class="line"><a name="l00718"></a><span class="lineno"> 718</span> </div><div class="line"><a name="l00719"></a><span class="lineno"> 719</span>  <span class="comment">/* Compute previous state-score + observation output prob for each emitting state */</span></div><div class="line"><a name="l00720"></a><span class="lineno"> 720</span>  ctx->st_sen_scr[0] = hmm_in_score(hmm) + hmm_senscr(hmm, 0);</div><div class="line"><a name="l00721"></a><span class="lineno"> 721</span>  <span class="keywordflow">for</span> (from = 1; from < hmm_n_emit_state(hmm); ++from) {</div><div class="line"><a name="l00722"></a><span class="lineno"> 722</span>  <span class="keywordflow">if</span> ((ctx->st_sen_scr[from] =</div><div class="line"><a name="l00723"></a><span class="lineno"> 723</span>  hmm_score(hmm, from) + hmm_senscr(hmm, from)) <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>)</div><div class="line"><a name="l00724"></a><span class="lineno"> 724</span>  ctx->st_sen_scr[from] = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00725"></a><span class="lineno"> 725</span>  }</div><div class="line"><a name="l00726"></a><span class="lineno"> 726</span> </div><div class="line"><a name="l00727"></a><span class="lineno"> 727</span>  <span class="comment">/* FIXME/TODO: Use the BLAS for all this. */</span></div><div class="line"><a name="l00728"></a><span class="lineno"> 728</span>  <span class="comment">/* Evaluate final-state first, which does not have a self-transition */</span></div><div class="line"><a name="l00729"></a><span class="lineno"> 729</span>  final_state = hmm_n_emit_state(hmm);</div><div class="line"><a name="l00730"></a><span class="lineno"> 730</span>  to = final_state;</div><div class="line"><a name="l00731"></a><span class="lineno"> 731</span>  scr = <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00732"></a><span class="lineno"> 732</span>  bestfrom = -1;</div><div class="line"><a name="l00733"></a><span class="lineno"> 733</span>  <span class="keywordflow">for</span> (from = to - 1; from >= 0; --from) {</div><div class="line"><a name="l00734"></a><span class="lineno"> 734</span>  <span class="keywordflow">if</span> ((hmm_tprob(hmm, from, to) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a9b38399b544dbb93bc9b7d0094e91db7">TMAT_WORST_SCORE</a>) &&</div><div class="line"><a name="l00735"></a><span class="lineno"> 735</span>  ((newscr = ctx->st_sen_scr[from]</div><div class="line"><a name="l00736"></a><span class="lineno"> 736</span>  + hmm_tprob(hmm, from, to)) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> scr)) {</div><div class="line"><a name="l00737"></a><span class="lineno"> 737</span>  scr = newscr;</div><div class="line"><a name="l00738"></a><span class="lineno"> 738</span>  bestfrom = from;</div><div class="line"><a name="l00739"></a><span class="lineno"> 739</span>  }</div><div class="line"><a name="l00740"></a><span class="lineno"> 740</span>  }</div><div class="line"><a name="l00741"></a><span class="lineno"> 741</span>  hmm_out_score(hmm) = scr;</div><div class="line"><a name="l00742"></a><span class="lineno"> 742</span>  <span class="keywordflow">if</span> (bestfrom >= 0)</div><div class="line"><a name="l00743"></a><span class="lineno"> 743</span>  hmm_out_history(hmm) = hmm_history(hmm, bestfrom);</div><div class="line"><a name="l00744"></a><span class="lineno"> 744</span>  bestscr = scr;</div><div class="line"><a name="l00745"></a><span class="lineno"> 745</span> </div><div class="line"><a name="l00746"></a><span class="lineno"> 746</span>  <span class="comment">/* Evaluate all other states, which might have self-transitions */</span></div><div class="line"><a name="l00747"></a><span class="lineno"> 747</span>  <span class="keywordflow">for</span> (to = final_state - 1; to >= 0; --to) {</div><div class="line"><a name="l00748"></a><span class="lineno"> 748</span>  <span class="comment">/* Score from self-transition, if any */</span></div><div class="line"><a name="l00749"></a><span class="lineno"> 749</span>  scr =</div><div class="line"><a name="l00750"></a><span class="lineno"> 750</span>  (hmm_tprob(hmm, to, to) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a9b38399b544dbb93bc9b7d0094e91db7">TMAT_WORST_SCORE</a>)</div><div class="line"><a name="l00751"></a><span class="lineno"> 751</span>  ? ctx->st_sen_scr[to] + hmm_tprob(hmm, to, to)</div><div class="line"><a name="l00752"></a><span class="lineno"> 752</span>  : <a class="code" href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a>;</div><div class="line"><a name="l00753"></a><span class="lineno"> 753</span> </div><div class="line"><a name="l00754"></a><span class="lineno"> 754</span>  <span class="comment">/* Scores from transitions from other states */</span></div><div class="line"><a name="l00755"></a><span class="lineno"> 755</span>  bestfrom = -1;</div><div class="line"><a name="l00756"></a><span class="lineno"> 756</span>  <span class="keywordflow">for</span> (from = to - 1; from >= 0; --from) {</div><div class="line"><a name="l00757"></a><span class="lineno"> 757</span>  <span class="keywordflow">if</span> ((hmm_tprob(hmm, from, to) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> <a class="code" href="hmm_8h.html#a9b38399b544dbb93bc9b7d0094e91db7">TMAT_WORST_SCORE</a>) &&</div><div class="line"><a name="l00758"></a><span class="lineno"> 758</span>  ((newscr = ctx->st_sen_scr[from]</div><div class="line"><a name="l00759"></a><span class="lineno"> 759</span>  + hmm_tprob(hmm, from, to)) <a class="code" href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a> scr)) {</div><div class="line"><a name="l00760"></a><span class="lineno"> 760</span>  scr = newscr;</div><div class="line"><a name="l00761"></a><span class="lineno"> 761</span>  bestfrom = from;</div><div class="line"><a name="l00762"></a><span class="lineno"> 762</span>  }</div><div class="line"><a name="l00763"></a><span class="lineno"> 763</span>  }</div><div class="line"><a name="l00764"></a><span class="lineno"> 764</span> </div><div class="line"><a name="l00765"></a><span class="lineno"> 765</span>  <span class="comment">/* Update new result for state to */</span></div><div class="line"><a name="l00766"></a><span class="lineno"> 766</span>  <span class="keywordflow">if</span> (to == 0) {</div><div class="line"><a name="l00767"></a><span class="lineno"> 767</span>  hmm_in_score(hmm) = scr;</div><div class="line"><a name="l00768"></a><span class="lineno"> 768</span>  <span class="keywordflow">if</span> (bestfrom >= 0)</div><div class="line"><a name="l00769"></a><span class="lineno"> 769</span>  hmm_in_history(hmm) = hmm_history(hmm, bestfrom);</div><div class="line"><a name="l00770"></a><span class="lineno"> 770</span>  }</div><div class="line"><a name="l00771"></a><span class="lineno"> 771</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00772"></a><span class="lineno"> 772</span>  hmm_score(hmm, to) = scr;</div><div class="line"><a name="l00773"></a><span class="lineno"> 773</span>  <span class="keywordflow">if</span> (bestfrom >= 0)</div><div class="line"><a name="l00774"></a><span class="lineno"> 774</span>  hmm_history(hmm, to) = hmm_history(hmm, bestfrom);</div><div class="line"><a name="l00775"></a><span class="lineno"> 775</span>  }</div><div class="line"><a name="l00776"></a><span class="lineno"> 776</span>  <span class="comment">/* Propagate ssid for multiplex HMMs */</span></div><div class="line"><a name="l00777"></a><span class="lineno"> 777</span>  <span class="keywordflow">if</span> (bestfrom >= 0 && hmm_is_mpx(hmm))</div><div class="line"><a name="l00778"></a><span class="lineno"> 778</span>  hmm->senid[to] = hmm->senid[bestfrom];</div><div class="line"><a name="l00779"></a><span class="lineno"> 779</span> </div><div class="line"><a name="l00780"></a><span class="lineno"> 780</span>  <span class="keywordflow">if</span> (bestscr <a class="code" href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a> scr)</div><div class="line"><a name="l00781"></a><span class="lineno"> 781</span>  bestscr = scr;</div><div class="line"><a name="l00782"></a><span class="lineno"> 782</span>  }</div><div class="line"><a name="l00783"></a><span class="lineno"> 783</span> </div><div class="line"><a name="l00784"></a><span class="lineno"> 784</span>  hmm_bestscore(hmm) = bestscr;</div><div class="line"><a name="l00785"></a><span class="lineno"> 785</span>  <span class="keywordflow">return</span> bestscr;</div><div class="line"><a name="l00786"></a><span class="lineno"> 786</span> }</div><div class="line"><a name="l00787"></a><span class="lineno"> 787</span> </div><div class="line"><a name="l00788"></a><span class="lineno"> 788</span> int32</div><div class="line"><a name="l00789"></a><span class="lineno"><a class="line" href="hmm_8h.html#a24ed030b10cb07e12173b45d3800db4b"> 789</a></span> <a class="code" href="hmm_8h.html#a24ed030b10cb07e12173b45d3800db4b">hmm_vit_eval</a>(<a class="code" href="structhmm__t.html">hmm_t</a> * hmm)</div><div class="line"><a name="l00790"></a><span class="lineno"> 790</span> {</div><div class="line"><a name="l00791"></a><span class="lineno"> 791</span>  <span class="keywordflow">if</span> (hmm_is_mpx(hmm)) {</div><div class="line"><a name="l00792"></a><span class="lineno"> 792</span>  <span class="keywordflow">if</span> (hmm_n_emit_state(hmm) == 5)</div><div class="line"><a name="l00793"></a><span class="lineno"> 793</span>  <span class="keywordflow">return</span> hmm_vit_eval_5st_lr_mpx(hmm);</div><div class="line"><a name="l00794"></a><span class="lineno"> 794</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (hmm_n_emit_state(hmm) == 3)</div><div class="line"><a name="l00795"></a><span class="lineno"> 795</span>  <span class="keywordflow">return</span> hmm_vit_eval_3st_lr_mpx(hmm);</div><div class="line"><a name="l00796"></a><span class="lineno"> 796</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00797"></a><span class="lineno"> 797</span>  <span class="keywordflow">return</span> hmm_vit_eval_anytopo(hmm);</div><div class="line"><a name="l00798"></a><span class="lineno"> 798</span>  }</div><div class="line"><a name="l00799"></a><span class="lineno"> 799</span>  <span class="keywordflow">else</span> {</div><div class="line"><a name="l00800"></a><span class="lineno"> 800</span>  <span class="keywordflow">if</span> (hmm_n_emit_state(hmm) == 5)</div><div class="line"><a name="l00801"></a><span class="lineno"> 801</span>  <span class="keywordflow">return</span> hmm_vit_eval_5st_lr(hmm);</div><div class="line"><a name="l00802"></a><span class="lineno"> 802</span>  <span class="keywordflow">else</span> <span class="keywordflow">if</span> (hmm_n_emit_state(hmm) == 3)</div><div class="line"><a name="l00803"></a><span class="lineno"> 803</span>  <span class="keywordflow">return</span> hmm_vit_eval_3st_lr(hmm);</div><div class="line"><a name="l00804"></a><span class="lineno"> 804</span>  <span class="keywordflow">else</span></div><div class="line"><a name="l00805"></a><span class="lineno"> 805</span>  <span class="keywordflow">return</span> hmm_vit_eval_anytopo(hmm);</div><div class="line"><a name="l00806"></a><span class="lineno"> 806</span>  }</div><div class="line"><a name="l00807"></a><span class="lineno"> 807</span> }</div><div class="line"><a name="l00808"></a><span class="lineno"> 808</span> </div><div class="line"><a name="l00809"></a><span class="lineno"> 809</span> int32</div><div class="line"><a name="l00810"></a><span class="lineno"><a class="line" href="hmm_8h.html#a84947383bf7940f799918c37ece85cf0"> 810</a></span> <a class="code" href="hmm_8h.html#a84947383bf7940f799918c37ece85cf0">hmm_dump_vit_eval</a>(<a class="code" href="structhmm__t.html">hmm_t</a> * hmm, FILE * fp)</div><div class="line"><a name="l00811"></a><span class="lineno"> 811</span> {</div><div class="line"><a name="l00812"></a><span class="lineno"> 812</span>  int32 bs = 0;</div><div class="line"><a name="l00813"></a><span class="lineno"> 813</span> </div><div class="line"><a name="l00814"></a><span class="lineno"> 814</span>  <span class="keywordflow">if</span> (fp) {</div><div class="line"><a name="l00815"></a><span class="lineno"> 815</span>  fprintf(fp, <span class="stringliteral">"BEFORE:\n"</span>);</div><div class="line"><a name="l00816"></a><span class="lineno"> 816</span>  <a class="code" href="hmm_8h.html#ad747fa967b5e414ad48fdffb9b767baf">hmm_dump</a>(hmm, fp);</div><div class="line"><a name="l00817"></a><span class="lineno"> 817</span>  }</div><div class="line"><a name="l00818"></a><span class="lineno"> 818</span>  bs = <a class="code" href="hmm_8h.html#a24ed030b10cb07e12173b45d3800db4b">hmm_vit_eval</a>(hmm);</div><div class="line"><a name="l00819"></a><span class="lineno"> 819</span>  <span class="keywordflow">if</span> (fp) {</div><div class="line"><a name="l00820"></a><span class="lineno"> 820</span>  fprintf(fp, <span class="stringliteral">"AFTER:\n"</span>);</div><div class="line"><a name="l00821"></a><span class="lineno"> 821</span>  <a class="code" href="hmm_8h.html#ad747fa967b5e414ad48fdffb9b767baf">hmm_dump</a>(hmm, fp);</div><div class="line"><a name="l00822"></a><span class="lineno"> 822</span>  }</div><div class="line"><a name="l00823"></a><span class="lineno"> 823</span> </div><div class="line"><a name="l00824"></a><span class="lineno"> 824</span>  <span class="keywordflow">return</span> bs;</div><div class="line"><a name="l00825"></a><span class="lineno"> 825</span> }</div><div class="ttc" id="hmm_8h_html_a84947383bf7940f799918c37ece85cf0"><div class="ttname"><a href="hmm_8h.html#a84947383bf7940f799918c37ece85cf0">hmm_dump_vit_eval</a></div><div class="ttdeci">int32 hmm_dump_vit_eval(hmm_t *hmm, FILE *fp)</div><div class="ttdoc">Like hmm_vit_eval, but dump HMM state and relevant senscr to fp first, for debugging;. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00810">hmm.c:810</a></div></div>
<div class="ttc" id="hmm_8h_html_aa911ae0d1c0eba562692fbeebca90d78"><div class="ttname"><a href="hmm_8h.html#aa911ae0d1c0eba562692fbeebca90d78">hmm_init</a></div><div class="ttdeci">void hmm_init(hmm_context_t *ctx, hmm_t *hmm, int mpx, int ssid, int tmatid)</div><div class="ttdoc">Populate a previously-allocated HMM structure, allocating internal data. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00089">hmm.c:89</a></div></div>
<div class="ttc" id="structhmm__t_html"><div class="ttname"><a href="structhmm__t.html">hmm_t</a></div><div class="ttdoc">An individual HMM among the HMM search space. </div></div>
<div class="ttc" id="hmm_8h_html_a7440ced1649225beb6816bf62481e08b"><div class="ttname"><a href="hmm_8h.html#a7440ced1649225beb6816bf62481e08b">hmm_deinit</a></div><div class="ttdeci">void hmm_deinit(hmm_t *hmm)</div><div class="ttdoc">Free an HMM structure, releasing internal data (but not the HMM structure itself). </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00111">hmm.c:111</a></div></div>
<div class="ttc" id="bin__mdef_8h_html_a8ee283c316e9f4aa8e6d18c1d44026bc"><div class="ttname"><a href="bin__mdef_8h.html#a8ee283c316e9f4aa8e6d18c1d44026bc">BAD_SSID</a></div><div class="ttdeci">#define BAD_SSID</div><div class="ttdoc">Invalid senone sequence ID (limited to 16 bits for PocketSphinx). </div><div class="ttdef"><b>Definition:</b> <a href="bin__mdef_8h_source.html#l00094">bin_mdef.h:94</a></div></div>
<div class="ttc" id="hmm_8h_html"><div class="ttname"><a href="hmm_8h.html">hmm.h</a></div><div class="ttdoc">Implementation of HMM base structure. </div></div>
<div class="ttc" id="hmm_8h_html_a1eb055ab0e55008f27d78e7b07a55a1c"><div class="ttname"><a href="hmm_8h.html#a1eb055ab0e55008f27d78e7b07a55a1c">HMM_MAX_NSTATE</a></div><div class="ttdeci">#define HMM_MAX_NSTATE</div><div class="ttdoc">Hard-coded limit on the number of emitting states. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8h_source.html#l00160">hmm.h:160</a></div></div>
<div class="ttc" id="hmm_8h_html_a24ed030b10cb07e12173b45d3800db4b"><div class="ttname"><a href="hmm_8h.html#a24ed030b10cb07e12173b45d3800db4b">hmm_vit_eval</a></div><div class="ttdeci">int32 hmm_vit_eval(hmm_t *hmm)</div><div class="ttdoc">Viterbi evaluation of given HMM. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00789">hmm.c:789</a></div></div>
<div class="ttc" id="hmm_8h_html_a0438bc7672ff9200274ffe7b5051eb92"><div class="ttname"><a href="hmm_8h.html#a0438bc7672ff9200274ffe7b5051eb92">hmm_normalize</a></div><div class="ttdeci">void hmm_normalize(hmm_t *h, int32 bestscr)</div><div class="ttdoc">Renormalize the scores in this HMM based on the given best score. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00209">hmm.c:209</a></div></div>
<div class="ttc" id="hmm_8h_html_a4d6e2799cbe290112e8517adcab1b038"><div class="ttname"><a href="hmm_8h.html#a4d6e2799cbe290112e8517adcab1b038">hmm_context_init</a></div><div class="ttdeci">hmm_context_t * hmm_context_init(int32 n_emit_state, uint8 **const *tp, int16 const *senscore, uint16 *const *sseq)</div><div class="ttdoc">Create an HMM context. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00056">hmm.c:56</a></div></div>
<div class="ttc" id="hmm_8h_html_a833f100ee293ad0f1c03f2a5ef9be77a"><div class="ttname"><a href="hmm_8h.html#a833f100ee293ad0f1c03f2a5ef9be77a">WORST_SCORE</a></div><div class="ttdeci">#define WORST_SCORE</div><div class="ttdoc">Large "bad" score. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8h_source.html#l00084">hmm.h:84</a></div></div>
<div class="ttc" id="structhmm__context__t_html"><div class="ttname"><a href="structhmm__context__t.html">hmm_context_t</a></div><div class="ttdoc">Shared information between a set of HMMs. </div></div>
<div class="ttc" id="hmm_8h_html_a7285d01d533996d750c78e0d96042716"><div class="ttname"><a href="hmm_8h.html#a7285d01d533996d750c78e0d96042716">hmm_enter</a></div><div class="ttdeci">void hmm_enter(hmm_t *h, int32 score, int32 histid, int frame)</div><div class="ttdoc">Enter an HMM with the given path score and history ID. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00201">hmm.c:201</a></div></div>
<div class="ttc" id="hmm_8h_html_ad747fa967b5e414ad48fdffb9b767baf"><div class="ttname"><a href="hmm_8h.html#ad747fa967b5e414ad48fdffb9b767baf">hmm_dump</a></div><div class="ttdeci">void hmm_dump(hmm_t *h, FILE *fp)</div><div class="ttdoc">For debugging, dump the whole HMM out. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00116">hmm.c:116</a></div></div>
<div class="ttc" id="hmm_8h_html_aa930fb8fb6fce7f34bcf4018b81d7066"><div class="ttname"><a href="hmm_8h.html#aa930fb8fb6fce7f34bcf4018b81d7066">WORSE_THAN</a></div><div class="ttdeci">#define WORSE_THAN</div><div class="ttdoc">Is one score worse than another? </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8h_source.html#l00100">hmm.h:100</a></div></div>
<div class="ttc" id="hmm_8h_html_af4c0cefb23087a0b1731b34048cfdaf9"><div class="ttname"><a href="hmm_8h.html#af4c0cefb23087a0b1731b34048cfdaf9">hmm_clear</a></div><div class="ttdeci">void hmm_clear(hmm_t *h)</div><div class="ttdoc">Reset the states of the HMM to the invalid condition. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00183">hmm.c:183</a></div></div>
<div class="ttc" id="hmm_8h_html_a9b38399b544dbb93bc9b7d0094e91db7"><div class="ttname"><a href="hmm_8h.html#a9b38399b544dbb93bc9b7d0094e91db7">TMAT_WORST_SCORE</a></div><div class="ttdeci">#define TMAT_WORST_SCORE</div><div class="ttdoc">Watch out, though! Transition matrix entries that are supposed to be "zero" don&#39;t actually get that s...</div><div class="ttdef"><b>Definition:</b> <a href="hmm_8h_source.html#l00090">hmm.h:90</a></div></div>
<div class="ttc" id="hmm_8h_html_a2874ab52613ff781c96f570ec0eb0d98"><div class="ttname"><a href="hmm_8h.html#a2874ab52613ff781c96f570ec0eb0d98">BETTER_THAN</a></div><div class="ttdeci">#define BETTER_THAN</div><div class="ttdoc">Is one score better than another? </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8h_source.html#l00095">hmm.h:95</a></div></div>
<div class="ttc" id="hmm_8h_html_a9561d7ffa1e61c99de2d2b900774152f"><div class="ttname"><a href="hmm_8h.html#a9561d7ffa1e61c99de2d2b900774152f">hmm_clear_scores</a></div><div class="ttdeci">void hmm_clear_scores(hmm_t *h)</div><div class="ttdoc">Reset the scores of the HMM. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00170">hmm.c:170</a></div></div>
<div class="ttc" id="hmm_8h_html_ab66534ad7970d49527f1b2a1e76bb05e"><div class="ttname"><a href="hmm_8h.html#ab66534ad7970d49527f1b2a1e76bb05e">hmm_context_free</a></div><div class="ttdeci">void hmm_context_free(hmm_context_t *ctx)</div><div class="ttdoc">Free an HMM context. </div><div class="ttdef"><b>Definition:</b> <a href="hmm_8c_source.html#l00080">hmm.c:80</a></div></div>
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