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<div class="title">SpectrumAlignment.h</div>  </div>
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<a href="SpectrumAlignment_8h.html">Go to the documentation of this file.</a><div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">//                   OpenMS -- Open-Source Mass Spectrometry</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">// ETH Zurich, and Freie Universitaet Berlin 2002-2013.</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">// This software is released under a three-clause BSD license:</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">//  * Redistributions of source code must retain the above copyright</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">//    notice, this list of conditions and the following disclaimer.</span></div>
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<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160;<span class="comment">//    documentation and/or other materials provided with the distribution.</span></div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="comment">//  * Neither the name of any author or any participating institution</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="comment">//    may be used to endorse or promote products derived from this software</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="comment">//    without specific prior written permission.</span></div>
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<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="comment">// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</span></div>
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<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="comment">// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</span></div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00030"></a><span class="lineno">   30</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;<span class="comment">// $Maintainer: Timo Sachsenberg $</span></div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;<span class="comment">// $Authors: Andreas Bertsch $</span></div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;<span class="comment">// --------------------------------------------------------------------------</span></div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;<span class="comment">//</span></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;<span class="preprocessor">#ifndef OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENT_H</span></div>
<div class="line"><a name="l00036"></a><span class="lineno">   36</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#define OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENT_H</span></div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160;<span class="preprocessor">#include &lt;<a class="code" href="DefaultParamHandler_8h.html">OpenMS/DATASTRUCTURES/DefaultParamHandler.h</a>&gt;</span></div>
<div class="line"><a name="l00039"></a><span class="lineno">   39</span>&#160;</div>
<div class="line"><a name="l00040"></a><span class="lineno">   40</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;<span class="preprocessor">#include &lt;map&gt;</span></div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;<span class="preprocessor">#include &lt;utility&gt;</span></div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160;<span class="preprocessor">#include &lt;algorithm&gt;</span></div>
<div class="line"><a name="l00044"></a><span class="lineno">   44</span>&#160;</div>
<div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="SpectrumAlignment_8h.html#a652ae64d2c029f80d2ab80e5e00665a6">   45</a></span>&#160;<span class="preprocessor">#define ALIGNMENT_DEBUG</span></div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#undef  ALIGNMENT_DEBUG</span></div>
<div class="line"><a name="l00047"></a><span class="lineno">   47</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00048"></a><span class="lineno">   48</span>&#160;<span class="keyword">namespace </span>OpenMS</div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;{</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;</div>
<div class="line"><a name="l00062"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectrumAlignment.html">   62</a></span>&#160;  <span class="keyword">class </span>OPENMS_DLLAPI <a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a> :</div>
<div class="line"><a name="l00063"></a><span class="lineno">   63</span>&#160;    <span class="keyword">public</span> <a class="code" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></div>
<div class="line"><a name="l00064"></a><span class="lineno">   64</span>&#160;  {</div>
<div class="line"><a name="l00065"></a><span class="lineno">   65</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00066"></a><span class="lineno">   66</span>&#160;</div>
<div class="line"><a name="l00067"></a><span class="lineno">   67</span>&#160;    <span class="comment">// @name Constructors and Destructors</span></div>
<div class="line"><a name="l00068"></a><span class="lineno">   68</span>&#160;    <span class="comment">// @{</span></div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;<span class="comment"></span>    <a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a>();</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160;</div>
<div class="line"><a name="l00073"></a><span class="lineno">   73</span>&#160;    <a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a>(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a> &amp; source);</div>
<div class="line"><a name="l00074"></a><span class="lineno">   74</span>&#160;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160;    <span class="keyword">virtual</span> ~<a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a>();</div>
<div class="line"><a name="l00077"></a><span class="lineno">   77</span>&#160;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160;    <a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a> &amp; operator=(<span class="keyword">const</span> <a class="code" href="classOpenMS_1_1SpectrumAlignment.html">SpectrumAlignment</a> &amp; source);</div>
<div class="line"><a name="l00080"></a><span class="lineno">   80</span>&#160;    <span class="comment">// @}</span></div>
<div class="line"><a name="l00081"></a><span class="lineno">   81</span>&#160;</div>
<div class="line"><a name="l00082"></a><span class="lineno">   82</span>&#160;    <span class="keyword">template</span> &lt;<span class="keyword">typename</span> SpectrumType&gt;</div>
<div class="line"><a name="l00083"></a><span class="lineno"><a class="line" href="classOpenMS_1_1SpectrumAlignment.html#a1e695a5349c395939217edc717effe84">   83</a></span>&#160;    <span class="keywordtype">void</span> <a class="code" href="classOpenMS_1_1SpectrumAlignment.html#a1e695a5349c395939217edc717effe84">getSpectrumAlignment</a>(std::vector&lt;std::pair&lt;Size, Size&gt; &gt; &amp; alignment, <span class="keyword">const</span> SpectrumType &amp; s1, <span class="keyword">const</span> SpectrumType &amp; s2)<span class="keyword"> const</span></div>
<div class="line"><a name="l00084"></a><span class="lineno">   84</span>&#160;<span class="keyword">    </span>{</div>
<div class="line"><a name="l00085"></a><span class="lineno">   85</span>&#160;      <span class="keywordflow">if</span> (!s1.isSorted() || !s2.isSorted())</div>
<div class="line"><a name="l00086"></a><span class="lineno">   86</span>&#160;      {</div>
<div class="line"><a name="l00087"></a><span class="lineno">   87</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1IllegalArgument.html">Exception::IllegalArgument</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__, <span class="stringliteral">&quot;Input to SpectrumAlignment is not sorted!&quot;</span>);</div>
<div class="line"><a name="l00088"></a><span class="lineno">   88</span>&#160;      }</div>
<div class="line"><a name="l00089"></a><span class="lineno">   89</span>&#160;      <span class="comment">// TODO remove parameter </span></div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;      <span class="keywordflow">if</span> (param_.getValue(<span class="stringliteral">&quot;is_relative_tolerance&quot;</span>).toBool() )</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;      {</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;        <span class="keywordflow">throw</span> <a class="code" href="classOpenMS_1_1Exception_1_1NotImplemented.html">Exception::NotImplemented</a>(__FILE__, __LINE__, __PRETTY_FUNCTION__);</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160;      }</div>
<div class="line"><a name="l00094"></a><span class="lineno">   94</span>&#160;</div>
<div class="line"><a name="l00095"></a><span class="lineno">   95</span>&#160;      <span class="comment">// clear result</span></div>
<div class="line"><a name="l00096"></a><span class="lineno">   96</span>&#160;      alignment.clear();</div>
<div class="line"><a name="l00097"></a><span class="lineno">   97</span>&#160;</div>
<div class="line"><a name="l00098"></a><span class="lineno">   98</span>&#160;      <span class="keywordtype">double</span> tolerance = (<a class="code" href="classdouble.html">double</a>)param_.getValue(<span class="stringliteral">&quot;tolerance&quot;</span>);</div>
<div class="line"><a name="l00099"></a><span class="lineno">   99</span>&#160;      std::map&lt;Size, std::map&lt;Size, std::pair&lt;Size, Size&gt; &gt; &gt; traceback;</div>
<div class="line"><a name="l00100"></a><span class="lineno">  100</span>&#160;      std::map&lt;Size, std::map&lt;Size, double&gt; &gt; matrix;</div>
<div class="line"><a name="l00101"></a><span class="lineno">  101</span>&#160;</div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;      <span class="comment">// init the matrix with &quot;gap costs&quot; tolerance</span></div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;      matrix[0][0] = 0;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 1; i &lt;= s1.size(); ++i)</div>
<div class="line"><a name="l00105"></a><span class="lineno">  105</span>&#160;      {</div>
<div class="line"><a name="l00106"></a><span class="lineno">  106</span>&#160;        matrix[i][0] = i * tolerance;</div>
<div class="line"><a name="l00107"></a><span class="lineno">  107</span>&#160;        traceback[i][0]  = std::make_pair(i - 1, 0);</div>
<div class="line"><a name="l00108"></a><span class="lineno">  108</span>&#160;      }</div>
<div class="line"><a name="l00109"></a><span class="lineno">  109</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 1; j &lt;= s2.size(); ++j)</div>
<div class="line"><a name="l00110"></a><span class="lineno">  110</span>&#160;      {</div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;        matrix[0][j] = j * tolerance;</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;        traceback[0][j] = std::make_pair(0, j - 1);</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160;      }</div>
<div class="line"><a name="l00114"></a><span class="lineno">  114</span>&#160;</div>
<div class="line"><a name="l00115"></a><span class="lineno">  115</span>&#160;      <span class="comment">// fill in the matrix</span></div>
<div class="line"><a name="l00116"></a><span class="lineno">  116</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> left_ptr(1);</div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> last_i(0), last_j(0);</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160;</div>
<div class="line"><a name="l00119"></a><span class="lineno">  119</span>&#160;      <span class="comment">//Size off_band_counter(0);</span></div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 1; i &lt;= s1.size(); ++i)</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;      {</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160;        <span class="keywordtype">double</span> pos1(s1[i - 1].getMZ());</div>
<div class="line"><a name="l00123"></a><span class="lineno">  123</span>&#160;</div>
<div class="line"><a name="l00124"></a><span class="lineno">  124</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = left_ptr; j &lt;= s2.size(); ++j)</div>
<div class="line"><a name="l00125"></a><span class="lineno">  125</span>&#160;        {</div>
<div class="line"><a name="l00126"></a><span class="lineno">  126</span>&#160;          <span class="keywordtype">bool</span> off_band(<span class="keyword">false</span>);</div>
<div class="line"><a name="l00127"></a><span class="lineno">  127</span>&#160;          <span class="comment">// find min of the three possible directions</span></div>
<div class="line"><a name="l00128"></a><span class="lineno">  128</span>&#160;          <span class="keywordtype">double</span> pos2(s2[j - 1].getMZ());</div>
<div class="line"><a name="l00129"></a><span class="lineno">  129</span>&#160;          <span class="keywordtype">double</span> diff_align = fabs(pos1 - pos2);</div>
<div class="line"><a name="l00130"></a><span class="lineno">  130</span>&#160;</div>
<div class="line"><a name="l00131"></a><span class="lineno">  131</span>&#160;          <span class="comment">// running off the right border of the band?</span></div>
<div class="line"><a name="l00132"></a><span class="lineno">  132</span>&#160;          <span class="keywordflow">if</span> (pos2 &gt; pos1 &amp;&amp; diff_align &gt; tolerance)</div>
<div class="line"><a name="l00133"></a><span class="lineno">  133</span>&#160;          {</div>
<div class="line"><a name="l00134"></a><span class="lineno">  134</span>&#160;            <span class="keywordflow">if</span> (i &lt; s1.size() &amp;&amp; j &lt; s2.size() &amp;&amp; s1[i].getMZ() &lt; pos2)</div>
<div class="line"><a name="l00135"></a><span class="lineno">  135</span>&#160;            {</div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;              off_band = <span class="keyword">true</span>;</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;            }</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;          }</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;          <span class="comment">// can we tighten the left border of the band?</span></div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;          <span class="keywordflow">if</span> (pos1 &gt; pos2 &amp;&amp; diff_align &gt; tolerance &amp;&amp; j &gt; left_ptr + 1)</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;          {</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;            ++left_ptr;</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;          }</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160;</div>
<div class="line"><a name="l00146"></a><span class="lineno">  146</span>&#160;          <span class="keywordtype">double</span> score_align = diff_align;</div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160;</div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;          <span class="keywordflow">if</span> (matrix.find(i - 1) != matrix.end() &amp;&amp; matrix[i - 1].find(j - 1) != matrix[i - 1].end())</div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160;          {</div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;            score_align += matrix[i - 1][j - 1];</div>
<div class="line"><a name="l00151"></a><span class="lineno">  151</span>&#160;          }</div>
<div class="line"><a name="l00152"></a><span class="lineno">  152</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l00153"></a><span class="lineno">  153</span>&#160;          {</div>
<div class="line"><a name="l00154"></a><span class="lineno">  154</span>&#160;            score_align += (i - 1 + j - 1) * tolerance;</div>
<div class="line"><a name="l00155"></a><span class="lineno">  155</span>&#160;          }</div>
<div class="line"><a name="l00156"></a><span class="lineno">  156</span>&#160;</div>
<div class="line"><a name="l00157"></a><span class="lineno">  157</span>&#160;          <span class="keywordtype">double</span> score_up = tolerance;</div>
<div class="line"><a name="l00158"></a><span class="lineno">  158</span>&#160;          <span class="keywordflow">if</span> (matrix.find(i) != matrix.end() &amp;&amp; matrix[i].find(j - 1) != matrix[i].end())</div>
<div class="line"><a name="l00159"></a><span class="lineno">  159</span>&#160;          {</div>
<div class="line"><a name="l00160"></a><span class="lineno">  160</span>&#160;            score_up += matrix[i][j - 1];</div>
<div class="line"><a name="l00161"></a><span class="lineno">  161</span>&#160;          }</div>
<div class="line"><a name="l00162"></a><span class="lineno">  162</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l00163"></a><span class="lineno">  163</span>&#160;          {</div>
<div class="line"><a name="l00164"></a><span class="lineno">  164</span>&#160;            score_up += (i + j - 1) * tolerance;</div>
<div class="line"><a name="l00165"></a><span class="lineno">  165</span>&#160;          }</div>
<div class="line"><a name="l00166"></a><span class="lineno">  166</span>&#160;</div>
<div class="line"><a name="l00167"></a><span class="lineno">  167</span>&#160;          <span class="keywordtype">double</span> score_left = tolerance;</div>
<div class="line"><a name="l00168"></a><span class="lineno">  168</span>&#160;          <span class="keywordflow">if</span> (matrix.find(i - 1) != matrix.end() &amp;&amp; matrix[i - 1].find(j) != matrix[i - 1].end())</div>
<div class="line"><a name="l00169"></a><span class="lineno">  169</span>&#160;          {</div>
<div class="line"><a name="l00170"></a><span class="lineno">  170</span>&#160;            score_left += matrix[i - 1][j];</div>
<div class="line"><a name="l00171"></a><span class="lineno">  171</span>&#160;          }</div>
<div class="line"><a name="l00172"></a><span class="lineno">  172</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l00173"></a><span class="lineno">  173</span>&#160;          {</div>
<div class="line"><a name="l00174"></a><span class="lineno">  174</span>&#160;            score_left += (i - 1 + j) * tolerance;</div>
<div class="line"><a name="l00175"></a><span class="lineno">  175</span>&#160;          }</div>
<div class="line"><a name="l00176"></a><span class="lineno">  176</span>&#160;</div>
<div class="line"><a name="l00177"></a><span class="lineno">  177</span>&#160;<span class="preprocessor">#ifdef ALIGNMENT_DEBUG</span></div>
<div class="line"><a name="l00178"></a><span class="lineno">  178</span>&#160;<span class="preprocessor"></span>          cerr &lt;&lt; i &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; j &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; left_ptr &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; pos1 &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; pos2 &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; score_align &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; score_left &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; score_up &lt;&lt; endl;</div>
<div class="line"><a name="l00179"></a><span class="lineno">  179</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00180"></a><span class="lineno">  180</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00181"></a><span class="lineno">  181</span>&#160;          <span class="keywordflow">if</span> (score_align &lt;= score_up &amp;&amp; score_align &lt;= score_left &amp;&amp; diff_align &lt;= tolerance)</div>
<div class="line"><a name="l00182"></a><span class="lineno">  182</span>&#160;          {</div>
<div class="line"><a name="l00183"></a><span class="lineno">  183</span>&#160;            matrix[i][j] = score_align;</div>
<div class="line"><a name="l00184"></a><span class="lineno">  184</span>&#160;            traceback[i][j] = std::make_pair(i - 1, j - 1);</div>
<div class="line"><a name="l00185"></a><span class="lineno">  185</span>&#160;            last_i = i;</div>
<div class="line"><a name="l00186"></a><span class="lineno">  186</span>&#160;            last_j = j;</div>
<div class="line"><a name="l00187"></a><span class="lineno">  187</span>&#160;          }</div>
<div class="line"><a name="l00188"></a><span class="lineno">  188</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l00189"></a><span class="lineno">  189</span>&#160;          {</div>
<div class="line"><a name="l00190"></a><span class="lineno">  190</span>&#160;            <span class="keywordflow">if</span> (score_up &lt;= score_left)</div>
<div class="line"><a name="l00191"></a><span class="lineno">  191</span>&#160;            {</div>
<div class="line"><a name="l00192"></a><span class="lineno">  192</span>&#160;              matrix[i][j] = score_up;</div>
<div class="line"><a name="l00193"></a><span class="lineno">  193</span>&#160;              traceback[i][j] = std::make_pair(i, j - 1);</div>
<div class="line"><a name="l00194"></a><span class="lineno">  194</span>&#160;            }</div>
<div class="line"><a name="l00195"></a><span class="lineno">  195</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l00196"></a><span class="lineno">  196</span>&#160;            {</div>
<div class="line"><a name="l00197"></a><span class="lineno">  197</span>&#160;              matrix[i][j] = score_left;</div>
<div class="line"><a name="l00198"></a><span class="lineno">  198</span>&#160;              traceback[i][j] = std::make_pair(i - 1, j);</div>
<div class="line"><a name="l00199"></a><span class="lineno">  199</span>&#160;            }</div>
<div class="line"><a name="l00200"></a><span class="lineno">  200</span>&#160;          }</div>
<div class="line"><a name="l00201"></a><span class="lineno">  201</span>&#160;</div>
<div class="line"><a name="l00202"></a><span class="lineno">  202</span>&#160;          <span class="keywordflow">if</span> (off_band)</div>
<div class="line"><a name="l00203"></a><span class="lineno">  203</span>&#160;          {</div>
<div class="line"><a name="l00204"></a><span class="lineno">  204</span>&#160;            <span class="keywordflow">break</span>;</div>
<div class="line"><a name="l00205"></a><span class="lineno">  205</span>&#160;          }</div>
<div class="line"><a name="l00206"></a><span class="lineno">  206</span>&#160;        }</div>
<div class="line"><a name="l00207"></a><span class="lineno">  207</span>&#160;      }</div>
<div class="line"><a name="l00208"></a><span class="lineno">  208</span>&#160;</div>
<div class="line"><a name="l00209"></a><span class="lineno">  209</span>&#160;      <span class="comment">//last_i = s1.size() + 1;</span></div>
<div class="line"><a name="l00210"></a><span class="lineno">  210</span>&#160;      <span class="comment">//last_j = s2.size() + 1;</span></div>
<div class="line"><a name="l00211"></a><span class="lineno">  211</span>&#160;</div>
<div class="line"><a name="l00212"></a><span class="lineno">  212</span>&#160;      <span class="comment">//cerr &lt;&lt; last_i &lt;&lt; &quot; &quot; &lt;&lt; last_j &lt;&lt; endl;</span></div>
<div class="line"><a name="l00213"></a><span class="lineno">  213</span>&#160;</div>
<div class="line"><a name="l00214"></a><span class="lineno">  214</span>&#160;<span class="preprocessor">#ifdef ALIGNMENT_DEBUG</span></div>
<div class="line"><a name="l00215"></a><span class="lineno">  215</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#if 0</span></div>
<div class="line"><a name="l00216"></a><span class="lineno">  216</span>&#160;<span class="preprocessor"></span>      cerr &lt;&lt; <span class="stringliteral">&quot;TheMatrix: &quot;</span> &lt;&lt; endl &lt;&lt; <span class="stringliteral">&quot; \t  \t&quot;</span>;</div>
<div class="line"><a name="l00217"></a><span class="lineno">  217</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j != s2.size(); ++j)</div>
<div class="line"><a name="l00218"></a><span class="lineno">  218</span>&#160;      {</div>
<div class="line"><a name="l00219"></a><span class="lineno">  219</span>&#160;        cerr &lt;&lt; s2[j].getPosition()[0] &lt;&lt; <span class="stringliteral">&quot; \t&quot;</span>;</div>
<div class="line"><a name="l00220"></a><span class="lineno">  220</span>&#160;      }</div>
<div class="line"><a name="l00221"></a><span class="lineno">  221</span>&#160;      cerr &lt;&lt; endl;</div>
<div class="line"><a name="l00222"></a><span class="lineno">  222</span>&#160;      <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = 0; i &lt;= s1.size(); ++i)</div>
<div class="line"><a name="l00223"></a><span class="lineno">  223</span>&#160;      {</div>
<div class="line"><a name="l00224"></a><span class="lineno">  224</span>&#160;        <span class="keywordflow">if</span> (i != 0)</div>
<div class="line"><a name="l00225"></a><span class="lineno">  225</span>&#160;        {</div>
<div class="line"><a name="l00226"></a><span class="lineno">  226</span>&#160;          cerr &lt;&lt; s1[i - 1].getPosition()[0] &lt;&lt; <span class="stringliteral">&quot; \t&quot;</span>;</div>
<div class="line"><a name="l00227"></a><span class="lineno">  227</span>&#160;        }</div>
<div class="line"><a name="l00228"></a><span class="lineno">  228</span>&#160;        <span class="keywordflow">else</span></div>
<div class="line"><a name="l00229"></a><span class="lineno">  229</span>&#160;        {</div>
<div class="line"><a name="l00230"></a><span class="lineno">  230</span>&#160;          cerr &lt;&lt; <span class="stringliteral">&quot; \t&quot;</span>;</div>
<div class="line"><a name="l00231"></a><span class="lineno">  231</span>&#160;        }</div>
<div class="line"><a name="l00232"></a><span class="lineno">  232</span>&#160;        <span class="keywordflow">for</span> (<a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = 0; j &lt;= s2.size(); ++j)</div>
<div class="line"><a name="l00233"></a><span class="lineno">  233</span>&#160;        {</div>
<div class="line"><a name="l00234"></a><span class="lineno">  234</span>&#160;          <span class="keywordflow">if</span> (matrix.has(i) &amp;&amp; matrix[i].has(j))</div>
<div class="line"><a name="l00235"></a><span class="lineno">  235</span>&#160;          {</div>
<div class="line"><a name="l00236"></a><span class="lineno">  236</span>&#160;            <span class="keywordflow">if</span> (traceback[i][j].first == i - 1 &amp;&amp; traceback[i][j].second == j - 1)</div>
<div class="line"><a name="l00237"></a><span class="lineno">  237</span>&#160;            {</div>
<div class="line"><a name="l00238"></a><span class="lineno">  238</span>&#160;              cerr &lt;&lt; <span class="stringliteral">&quot;\\&quot;</span>;</div>
<div class="line"><a name="l00239"></a><span class="lineno">  239</span>&#160;            }</div>
<div class="line"><a name="l00240"></a><span class="lineno">  240</span>&#160;            <span class="keywordflow">else</span></div>
<div class="line"><a name="l00241"></a><span class="lineno">  241</span>&#160;            {</div>
<div class="line"><a name="l00242"></a><span class="lineno">  242</span>&#160;              <span class="keywordflow">if</span> (traceback[i][j].first == i - 1 &amp;&amp; traceback[i][j].second == j)</div>
<div class="line"><a name="l00243"></a><span class="lineno">  243</span>&#160;              {</div>
<div class="line"><a name="l00244"></a><span class="lineno">  244</span>&#160;                cerr &lt;&lt; <span class="stringliteral">&quot;|&quot;</span>;</div>
<div class="line"><a name="l00245"></a><span class="lineno">  245</span>&#160;              }</div>
<div class="line"><a name="l00246"></a><span class="lineno">  246</span>&#160;              <span class="keywordflow">else</span></div>
<div class="line"><a name="l00247"></a><span class="lineno">  247</span>&#160;              {</div>
<div class="line"><a name="l00248"></a><span class="lineno">  248</span>&#160;                cerr &lt;&lt; <span class="stringliteral">&quot;-&quot;</span>;</div>
<div class="line"><a name="l00249"></a><span class="lineno">  249</span>&#160;              }</div>
<div class="line"><a name="l00250"></a><span class="lineno">  250</span>&#160;            }</div>
<div class="line"><a name="l00251"></a><span class="lineno">  251</span>&#160;</div>
<div class="line"><a name="l00252"></a><span class="lineno">  252</span>&#160;            cerr &lt;&lt; matrix[i][j] &lt;&lt; <span class="stringliteral">&quot;  \t&quot;</span>;</div>
<div class="line"><a name="l00253"></a><span class="lineno">  253</span>&#160;          }</div>
<div class="line"><a name="l00254"></a><span class="lineno">  254</span>&#160;          <span class="keywordflow">else</span></div>
<div class="line"><a name="l00255"></a><span class="lineno">  255</span>&#160;          {</div>
<div class="line"><a name="l00256"></a><span class="lineno">  256</span>&#160;            cerr &lt;&lt; <span class="stringliteral">&quot;-1  \t&quot;</span>;</div>
<div class="line"><a name="l00257"></a><span class="lineno">  257</span>&#160;          }</div>
<div class="line"><a name="l00258"></a><span class="lineno">  258</span>&#160;        }</div>
<div class="line"><a name="l00259"></a><span class="lineno">  259</span>&#160;        cerr &lt;&lt; endl;</div>
<div class="line"><a name="l00260"></a><span class="lineno">  260</span>&#160;      }</div>
<div class="line"><a name="l00261"></a><span class="lineno">  261</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00262"></a><span class="lineno">  262</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00263"></a><span class="lineno">  263</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00264"></a><span class="lineno">  264</span>&#160;      <span class="comment">// do traceback</span></div>
<div class="line"><a name="l00265"></a><span class="lineno">  265</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i = last_i;</div>
<div class="line"><a name="l00266"></a><span class="lineno">  266</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> j = last_j;</div>
<div class="line"><a name="l00267"></a><span class="lineno">  267</span>&#160;</div>
<div class="line"><a name="l00268"></a><span class="lineno">  268</span>&#160;      <span class="keywordflow">while</span> (i &gt;= 1 &amp;&amp; j &gt;= 1)</div>
<div class="line"><a name="l00269"></a><span class="lineno">  269</span>&#160;      {</div>
<div class="line"><a name="l00270"></a><span class="lineno">  270</span>&#160;        <span class="keywordflow">if</span> (traceback[i][j].first == i - 1 &amp;&amp; traceback[i][j].second == j - 1)</div>
<div class="line"><a name="l00271"></a><span class="lineno">  271</span>&#160;        {</div>
<div class="line"><a name="l00272"></a><span class="lineno">  272</span>&#160;          alignment.push_back(std::make_pair(i - 1, j - 1));</div>
<div class="line"><a name="l00273"></a><span class="lineno">  273</span>&#160;        }</div>
<div class="line"><a name="l00274"></a><span class="lineno">  274</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> new_i = traceback[i][j].first;</div>
<div class="line"><a name="l00275"></a><span class="lineno">  275</span>&#160;        <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> new_j = traceback[i][j].second;</div>
<div class="line"><a name="l00276"></a><span class="lineno">  276</span>&#160;</div>
<div class="line"><a name="l00277"></a><span class="lineno">  277</span>&#160;        i = new_i;</div>
<div class="line"><a name="l00278"></a><span class="lineno">  278</span>&#160;        j = new_j;</div>
<div class="line"><a name="l00279"></a><span class="lineno">  279</span>&#160;      }</div>
<div class="line"><a name="l00280"></a><span class="lineno">  280</span>&#160;</div>
<div class="line"><a name="l00281"></a><span class="lineno">  281</span>&#160;      std::reverse(alignment.begin(), alignment.end());</div>
<div class="line"><a name="l00282"></a><span class="lineno">  282</span>&#160;</div>
<div class="line"><a name="l00283"></a><span class="lineno">  283</span>&#160;<span class="preprocessor">#ifdef ALIGNMENT_DEBUG</span></div>
<div class="line"><a name="l00284"></a><span class="lineno">  284</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#if 0</span></div>
<div class="line"><a name="l00285"></a><span class="lineno">  285</span>&#160;<span class="preprocessor"></span>      <span class="comment">// print alignment</span></div>
<div class="line"><a name="l00286"></a><span class="lineno">  286</span>&#160;      cerr &lt;&lt; <span class="stringliteral">&quot;Alignment (size=&quot;</span> &lt;&lt; alignment.size() &lt;&lt; <span class="stringliteral">&quot;): &quot;</span> &lt;&lt; endl;</div>
<div class="line"><a name="l00287"></a><span class="lineno">  287</span>&#160;</div>
<div class="line"><a name="l00288"></a><span class="lineno">  288</span>&#160;      <a class="code" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> i_s1(0), i_s2(0);</div>
<div class="line"><a name="l00289"></a><span class="lineno">  289</span>&#160;      <span class="keywordflow">for</span> (vector&lt;pair&lt;Size, Size&gt; &gt;::const_reverse_iterator it = alignment.rbegin(); it != alignment.rend(); ++it, ++i_s1, ++i_s2)</div>
<div class="line"><a name="l00290"></a><span class="lineno">  290</span>&#160;      {</div>
<div class="line"><a name="l00291"></a><span class="lineno">  291</span>&#160;        <span class="keywordflow">while</span> (i_s1 &lt; it-&gt;first - 1)</div>
<div class="line"><a name="l00292"></a><span class="lineno">  292</span>&#160;        {</div>
<div class="line"><a name="l00293"></a><span class="lineno">  293</span>&#160;          cerr &lt;&lt; i_s1 &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; s1[i_s1].getPosition()[0] &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; s1[i_s1].getIntensity() &lt;&lt; endl;</div>
<div class="line"><a name="l00294"></a><span class="lineno">  294</span>&#160;          i_s1++;</div>
<div class="line"><a name="l00295"></a><span class="lineno">  295</span>&#160;        }</div>
<div class="line"><a name="l00296"></a><span class="lineno">  296</span>&#160;        <span class="keywordflow">while</span> (i_s2 &lt; it-&gt;second - 1)</div>
<div class="line"><a name="l00297"></a><span class="lineno">  297</span>&#160;        {</div>
<div class="line"><a name="l00298"></a><span class="lineno">  298</span>&#160;          cerr &lt;&lt; <span class="stringliteral">&quot; \t &quot;</span> &lt;&lt;  i_s2 &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; s2[i_s2].getPosition()[0] &lt;&lt; <span class="stringliteral">&quot; &quot;</span> &lt;&lt; s2[i_s2].getIntensity() &lt;&lt; endl;</div>
<div class="line"><a name="l00299"></a><span class="lineno">  299</span>&#160;          i_s2++;</div>
<div class="line"><a name="l00300"></a><span class="lineno">  300</span>&#160;        }</div>
<div class="line"><a name="l00301"></a><span class="lineno">  301</span>&#160;        cerr &lt;&lt; <span class="stringliteral">&quot;(&quot;</span> &lt;&lt; s1[it-&gt;first - 1].getPosition()[0] &lt;&lt; <span class="stringliteral">&quot; &lt;-&gt; &quot;</span> &lt;&lt; s2[it-&gt;second - 1].getPosition()[0] &lt;&lt; <span class="stringliteral">&quot;) (&quot;</span></div>
<div class="line"><a name="l00302"></a><span class="lineno">  302</span>&#160;             &lt;&lt; it-&gt;first &lt;&lt; <span class="stringliteral">&quot;|&quot;</span> &lt;&lt; it-&gt;second &lt;&lt; <span class="stringliteral">&quot;) (&quot;</span> &lt;&lt; s1[it-&gt;first - 1].getIntensity() &lt;&lt; <span class="stringliteral">&quot;|&quot;</span> &lt;&lt; s2[it-&gt;second - 1].getIntensity() &lt;&lt; <span class="stringliteral">&quot;)&quot;</span> &lt;&lt; endl;</div>
<div class="line"><a name="l00303"></a><span class="lineno">  303</span>&#160;      }</div>
<div class="line"><a name="l00304"></a><span class="lineno">  304</span>&#160;<span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00305"></a><span class="lineno">  305</span>&#160;<span class="preprocessor"></span><span class="preprocessor">#endif</span></div>
<div class="line"><a name="l00306"></a><span class="lineno">  306</span>&#160;<span class="preprocessor"></span></div>
<div class="line"><a name="l00307"></a><span class="lineno">  307</span>&#160;    }</div>
<div class="line"><a name="l00308"></a><span class="lineno">  308</span>&#160;</div>
<div class="line"><a name="l00309"></a><span class="lineno">  309</span>&#160;  };</div>
<div class="line"><a name="l00310"></a><span class="lineno">  310</span>&#160;</div>
<div class="line"><a name="l00311"></a><span class="lineno">  311</span>&#160;}</div>
<div class="line"><a name="l00312"></a><span class="lineno">  312</span>&#160;<span class="preprocessor">#endif //OPENMS_COMPARISON_SPECTRA_SPECTRUMALIGNMENT_H</span></div>
<div class="ttc" id="classdouble_html"><div class="ttname"><a href="classdouble.html">double</a></div></div>
<div class="ttc" id="DefaultParamHandler_8h_html"><div class="ttname"><a href="DefaultParamHandler_8h.html">DefaultParamHandler.h</a></div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1IllegalArgument_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1IllegalArgument.html">OpenMS::Exception::IllegalArgument</a></div><div class="ttdoc">A method or algorithm argument contains illegal values. </div><div class="ttdef"><b>Definition:</b> Exception.h:634</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumAlignment_html"><div class="ttname"><a href="classOpenMS_1_1SpectrumAlignment.html">OpenMS::SpectrumAlignment</a></div><div class="ttdoc">Aligns the peaks of two spectra. </div><div class="ttdef"><b>Definition:</b> SpectrumAlignment.h:62</div></div>
<div class="ttc" id="group__Concept_html_gaf9ecec2d692138fab9167164a457cbd4"><div class="ttname"><a href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">OpenMS::Size</a></div><div class="ttdeci">size_t Size</div><div class="ttdoc">Size type e.g. used as variable which can hold result of size() </div><div class="ttdef"><b>Definition:</b> Types.h:144</div></div>
<div class="ttc" id="classOpenMS_1_1DefaultParamHandler_html"><div class="ttname"><a href="classOpenMS_1_1DefaultParamHandler.html">OpenMS::DefaultParamHandler</a></div><div class="ttdoc">A base class for all classes handling default parameters. </div><div class="ttdef"><b>Definition:</b> DefaultParamHandler.h:90</div></div>
<div class="ttc" id="classOpenMS_1_1SpectrumAlignment_html_a1e695a5349c395939217edc717effe84"><div class="ttname"><a href="classOpenMS_1_1SpectrumAlignment.html#a1e695a5349c395939217edc717effe84">OpenMS::SpectrumAlignment::getSpectrumAlignment</a></div><div class="ttdeci">void getSpectrumAlignment(std::vector&lt; std::pair&lt; Size, Size &gt; &gt; &amp;alignment, const SpectrumType &amp;s1, const SpectrumType &amp;s2) const </div><div class="ttdef"><b>Definition:</b> SpectrumAlignment.h:83</div></div>
<div class="ttc" id="classOpenMS_1_1Exception_1_1NotImplemented_html"><div class="ttname"><a href="classOpenMS_1_1Exception_1_1NotImplemented.html">OpenMS::Exception::NotImplemented</a></div><div class="ttdoc">Not implemented exception. </div><div class="ttdef"><b>Definition:</b> Exception.h:437</div></div>
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