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<div class="title">composition_constants.h File Reference</div> </div>
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<p>Constants used in compositional score matrix adjustment.
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<div class="textblock"><code>#include <<a class="el" href="ncbi__std_8h_source.html">algo/blast/core/ncbi_std.h</a>></code><br />
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<p><a href="composition__constants_8h_source.html">Go to the source code of this file.</a>
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Macros</h2></td></tr>
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<tr class="memitem:acd222382ee1d2c224057e6b67a245eaa"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="composition__constants_8h.html#acd222382ee1d2c224057e6b67a245eaa">COMPO_SCORE_MIN</a>   <a class="el" href="group__CToolsBridge.html#gacb121621948e15398f6f61838729535d">INT2_MIN</a></td></tr>
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<tr class="memdesc:acd222382ee1d2c224057e6b67a245eaa"><td class="mdescLeft"> </td><td class="mdescRight">Minimum score in a matrix. <a href="composition__constants_8h.html#acd222382ee1d2c224057e6b67a245eaa">More...</a><br /></td></tr>
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<tr class="memitem:a1855a5c3b56c369eef3f6486ece7f0c1"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="composition__constants_8h.html#a1855a5c3b56c369eef3f6486ece7f0c1">COMPO_NUM_TRUE_AA</a>   20</td></tr>
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<tr class="memdesc:a1855a5c3b56c369eef3f6486ece7f0c1"><td class="mdescLeft"> </td><td class="mdescRight">Number of standard amino acids. <a href="composition__constants_8h.html#a1855a5c3b56c369eef3f6486ece7f0c1">More...</a><br /></td></tr>
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<tr class="separator:a1855a5c3b56c369eef3f6486ece7f0c1"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a59d69cc69b551ac260854a15f81569b5"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="composition__constants_8h.html#a59d69cc69b551ac260854a15f81569b5">COMPO_LARGEST_ALPHABET</a>   28</td></tr>
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<tr class="memdesc:a59d69cc69b551ac260854a15f81569b5"><td class="mdescLeft"> </td><td class="mdescRight">The largest alphabet supported by this code (the code supports 26 or 28 character amino acid alphabets). <a href="composition__constants_8h.html#a59d69cc69b551ac260854a15f81569b5">More...</a><br /></td></tr>
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<tr class="memitem:ab5a7331cf976a99e5f421d5ff6617308"><td class="memItemLeft" align="right" valign="top">typedef enum <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbd">ECompoAdjustModes</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="composition__constants_8h.html#ab5a7331cf976a99e5f421d5ff6617308">ECompoAdjustModes</a></td></tr>
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<tr class="memdesc:ab5a7331cf976a99e5f421d5ff6617308"><td class="mdescLeft"> </td><td class="mdescRight">An collection of constants that specify all permissible modes of composition adjustment. <a href="composition__constants_8h.html#ab5a7331cf976a99e5f421d5ff6617308">More...</a><br /></td></tr>
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<tr class="memitem:a60688b7e672d87fc762814dee064e6aa"><td class="memItemLeft" align="right" valign="top">typedef enum <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7d">EMatrixAdjustRule</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="composition__constants_8h.html#a60688b7e672d87fc762814dee064e6aa">EMatrixAdjustRule</a></td></tr>
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<tr class="memdesc:a60688b7e672d87fc762814dee064e6aa"><td class="mdescLeft"> </td><td class="mdescRight">An collection of constants that specify all rules that may be used to generate a compositionally adjusted matrix. <a href="composition__constants_8h.html#a60688b7e672d87fc762814dee064e6aa">More...</a><br /></td></tr>
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Enumerations</h2></td></tr>
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<tr class="memitem:a13a00fe8dcff838754d4d76347612fbd"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbd">ECompoAdjustModes</a> { <br />
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  <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbda9d5ca0e176915ea8607c6c43ab2fe5c1">eNoCompositionBasedStats</a> = 0
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, <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbda5bdbfb18db42593b530a19e2ef77edff">eCompositionBasedStats</a> = 1
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, <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbdad9f13f92970b94d998b11cd1096f5506">eCompositionMatrixAdjust</a> = 2
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, <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbda709e522307ef4ff8e90105a2de3261e4">eCompoForceFullMatrixAdjust</a> = 3
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, <br />
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  <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbdae44d4f0461ac7fc6f7f014acf05701dd">eNumCompoAdjustModes</a>
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}</td></tr>
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<tr class="memdesc:a13a00fe8dcff838754d4d76347612fbd"><td class="mdescLeft"> </td><td class="mdescRight">An collection of constants that specify all permissible modes of composition adjustment. <a href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbd">More...</a><br /></td></tr>
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<tr class="memitem:a23ebbd0090320dd661c6861aed0cfa7d"><td class="memItemLeft" align="right" valign="top">enum  </td><td class="memItemRight" valign="bottom"><a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7d">EMatrixAdjustRule</a> { <br />
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  <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7da0b6d109c2571e7c5119ca4b1d4624468">eDontAdjustMatrix</a> = (-1)
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, <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7da219ddca1beed0e6f82bc56b728f812b1">eCompoScaleOldMatrix</a> = 0
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, <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7daf7b5bd0b853e642d74f9e50545829fb9">eUnconstrainedRelEntropy</a> = 1
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, <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7daaede6db91ee89073c49fe490979f6bb1">eRelEntropyOldMatrixNewContext</a> = 2
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, <br />
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  <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7da2fc3c35fb155868daf5f326c6d703b3c">eRelEntropyOldMatrixOldContext</a> = 3
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, <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7dab41dd3a3f717acc350f2853c437a7d66">eUserSpecifiedRelEntropy</a> = 4
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}</td></tr>
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<tr class="memdesc:a23ebbd0090320dd661c6861aed0cfa7d"><td class="mdescLeft"> </td><td class="mdescRight">An collection of constants that specify all rules that may be used to generate a compositionally adjusted matrix. <a href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7d">More...</a><br /></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Constants used in compositional score matrix adjustment. </p>
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<dl class="section author"><dt>Author</dt><dd>E. Michael Gertz, Alejandro Schaffer, Yi-Kuo Yu </dd></dl>
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<p class="definition">Definition in file <a class="el" href="composition__constants_8h_source.html">composition_constants.h</a>.</p>
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</div><h2 class="groupheader">Macro Definition Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a59d69cc69b551ac260854a15f81569b5">◆ </a></span>COMPO_LARGEST_ALPHABET</h2>
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<p>The largest alphabet supported by this code (the code supports 26 or 28 character amino acid alphabets). </p>
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<p>Used to specify the size of structures that are statically allocated. </p>
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<p class="definition">Definition at line <a class="el" href="composition__constants_8h_source.html#l00051">51</a> of file <a class="el" href="composition__constants_8h_source.html">composition_constants.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a1855a5c3b56c369eef3f6486ece7f0c1">◆ </a></span>COMPO_NUM_TRUE_AA</h2>
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<td class="memname">#define COMPO_NUM_TRUE_AA   20</td>
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<p>Number of standard amino acids. </p>
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<p class="definition">Definition at line <a class="el" href="composition__constants_8h_source.html#l00046">46</a> of file <a class="el" href="composition__constants_8h_source.html">composition_constants.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#acd222382ee1d2c224057e6b67a245eaa">◆ </a></span>COMPO_SCORE_MIN</h2>
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<td class="memname">#define COMPO_SCORE_MIN   <a class="el" href="group__CToolsBridge.html#gacb121621948e15398f6f61838729535d">INT2_MIN</a></td>
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<p>Minimum score in a matrix. </p>
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<p class="definition">Definition at line <a class="el" href="composition__constants_8h_source.html#l00043">43</a> of file <a class="el" href="composition__constants_8h_source.html">composition_constants.h</a>.</p>
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<h2 class="groupheader">Typedef Documentation</h2>
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<a id="ab5a7331cf976a99e5f421d5ff6617308"></a>
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<h2 class="memtitle"><span class="permalink"><a href="#ab5a7331cf976a99e5f421d5ff6617308">◆ </a></span>ECompoAdjustModes</h2>
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<td class="memname">typedef enum <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbd">ECompoAdjustModes</a> <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbd">ECompoAdjustModes</a></td>
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<p>An collection of constants that specify all permissible modes of composition adjustment. </p>
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<h2 class="memtitle"><span class="permalink"><a href="#a60688b7e672d87fc762814dee064e6aa">◆ </a></span>EMatrixAdjustRule</h2>
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<td class="memname">typedef enum <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7d">EMatrixAdjustRule</a> <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7d">EMatrixAdjustRule</a></td>
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<p>An collection of constants that specify all rules that may be used to generate a compositionally adjusted matrix. </p>
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<h2 class="groupheader">Enumeration Type Documentation</h2>
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<h2 class="memtitle"><span class="permalink"><a href="#a13a00fe8dcff838754d4d76347612fbd">◆ </a></span>ECompoAdjustModes</h2>
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<td class="memname">enum <a class="el" href="composition__constants_8h.html#a13a00fe8dcff838754d4d76347612fbd">ECompoAdjustModes</a></td>
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<p>An collection of constants that specify all permissible modes of composition adjustment. </p>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="a13a00fe8dcff838754d4d76347612fbda9d5ca0e176915ea8607c6c43ab2fe5c1"></a>eNoCompositionBasedStats </td><td class="fielddoc"><p>Don't use composition based statistics. </p>
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<tr><td class="fieldname"><a id="a13a00fe8dcff838754d4d76347612fbda5bdbfb18db42593b530a19e2ef77edff"></a>eCompositionBasedStats </td><td class="fielddoc"><p>Composition-based statistics as in NAR 29:2994-3005, 2001. </p>
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<tr><td class="fieldname"><a id="a13a00fe8dcff838754d4d76347612fbdad9f13f92970b94d998b11cd1096f5506"></a>eCompositionMatrixAdjust </td><td class="fielddoc"><p>Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties. </p>
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<p>Cannot be applied to PSSMs. </p>
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<tr><td class="fieldname"><a id="a13a00fe8dcff838754d4d76347612fbda709e522307ef4ff8e90105a2de3261e4"></a>eCompoForceFullMatrixAdjust </td><td class="fielddoc"><p>Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally. </p>
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<p>Cannot be applied to PSSMs. </p>
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<tr><td class="fieldname"><a id="a13a00fe8dcff838754d4d76347612fbdae44d4f0461ac7fc6f7f014acf05701dd"></a>eNumCompoAdjustModes </td><td class="fielddoc"></td></tr>
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<p class="definition">Definition at line <a class="el" href="composition__constants_8h_source.html#l00059">59</a> of file <a class="el" href="composition__constants_8h_source.html">composition_constants.h</a>.</p>
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<h2 class="memtitle"><span class="permalink"><a href="#a23ebbd0090320dd661c6861aed0cfa7d">◆ </a></span>EMatrixAdjustRule</h2>
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<td class="memname">enum <a class="el" href="composition__constants_8h.html#a23ebbd0090320dd661c6861aed0cfa7d">EMatrixAdjustRule</a></td>
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<p>An collection of constants that specify all rules that may be used to generate a compositionally adjusted matrix. </p>
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<tr><th colspan="2">Enumerator</th></tr><tr><td class="fieldname"><a id="a23ebbd0090320dd661c6861aed0cfa7da0b6d109c2571e7c5119ca4b1d4624468"></a>eDontAdjustMatrix </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a23ebbd0090320dd661c6861aed0cfa7da219ddca1beed0e6f82bc56b728f812b1"></a>eCompoScaleOldMatrix </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a23ebbd0090320dd661c6861aed0cfa7daf7b5bd0b853e642d74f9e50545829fb9"></a>eUnconstrainedRelEntropy </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a23ebbd0090320dd661c6861aed0cfa7daaede6db91ee89073c49fe490979f6bb1"></a>eRelEntropyOldMatrixNewContext </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a23ebbd0090320dd661c6861aed0cfa7da2fc3c35fb155868daf5f326c6d703b3c"></a>eRelEntropyOldMatrixOldContext </td><td class="fielddoc"></td></tr>
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<tr><td class="fieldname"><a id="a23ebbd0090320dd661c6861aed0cfa7dab41dd3a3f717acc350f2853c437a7d66"></a>eUserSpecifiedRelEntropy </td><td class="fielddoc"></td></tr>
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<p class="definition">Definition at line <a class="el" href="composition__constants_8h_source.html#l00076">76</a> of file <a class="el" href="composition__constants_8h_source.html">composition_constants.h</a>.</p>
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Generated by <a href="https://www.doxygen.org/index.html"><img class="footer" src="doxygen.svg" width="104" height="31" alt="doxygen"/></a> 1.9.0
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</small></address>
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<address style="align: right;"><small>Modified on Fri Sep 20 14:57:20 2024 by modify_doxy.py rev. 669887</small></address>
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