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+<div class="title">mainpage.h</div> </div>
+</div><!--header-->
+<div class="contents">
+<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> <span class="comment">/*</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"># The next comment is used to order the modules correctly #</span></div>
+<div class="line"><a name="l00004"></a><span class="lineno"> 4</span> <span class="comment">#############################################################</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> </div>
+<div class="line"><a name="l00108"></a><span class="lineno"> 108</span> <span class="comment">/*</span></div>
+<div class="line"><a name="l00109"></a><span class="lineno"> 109</span> <span class="comment">#############################################################</span></div>
+<div class="line"><a name="l00110"></a><span class="lineno"> 110</span> <span class="comment"># Now the mainpage text is following #</span></div>
+<div class="line"><a name="l00111"></a><span class="lineno"> 111</span> <span class="comment">#############################################################</span></div>
+<div class="line"><a name="l00112"></a><span class="lineno"> 112</span> <span class="comment">*/</span></div>
+<div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div>
+<div class="line"><a name="l00327"></a><span class="lineno"> 327</span>  { 0, 2, 2, 2, 2, 1, 1}, <span class="comment">/* Null replaced */</span></div>
+<div class="line"><a name="l00328"></a><span class="lineno"> 328</span>  { 2, 0, 2, 2, 2, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>}, <span class="comment">/* H replaced */</span></div>
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+<div class="line"><a name="l00332"></a><span class="lineno"> 332</span>  { 1, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 0, INF}, <span class="comment">/* S replaced */</span></div>
+<div class="line"><a name="l00333"></a><span class="lineno"> 333</span>  { 1, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 0}, <span class="comment">/* E replaced */</span></div>
+<div class="line"><a name="l00334"></a><span class="lineno"> 334</span> </div>
+<div class="line"><a name="l00335"></a><span class="lineno"> 335</span> </div>
+<div class="line"><a name="l00336"></a><span class="lineno"> 336</span> <span class="comment">/* Null, H, B, I, M, S, E */</span></div>
+<div class="line"><a name="l00337"></a><span class="lineno"> 337</span>  { 0, 100, 5, 5, 75, 5, 5}, <span class="comment">/* Null replaced */</span></div>
+<div class="line"><a name="l00338"></a><span class="lineno"> 338</span>  { 100, 0, 8, 8, 8, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>}, <span class="comment">/* H replaced */</span></div>
+<div class="line"><a name="l00339"></a><span class="lineno"> 339</span>  { 5, 8, 0, 3, 8, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>}, <span class="comment">/* B replaced */</span></div>
+<div class="line"><a name="l00340"></a><span class="lineno"> 340</span>  { 5, 8, 3, 0, 8, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>}, <span class="comment">/* I replaced */</span></div>
+<div class="line"><a name="l00341"></a><span class="lineno"> 341</span>  { 75, 8, 8, 8, 0, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>}, <span class="comment">/* M replaced */</span></div>
+<div class="line"><a name="l00342"></a><span class="lineno"> 342</span>  { 5, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 0, INF}, <span class="comment">/* S replaced */</span></div>
+<div class="line"><a name="l00343"></a><span class="lineno"> 343</span>  { 5, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, <a class="code" href="energy__const_8h.html#a12c2040f25d8e3a7b9e1c2024c618cb6">INF</a>, 0}, <span class="comment">/* E replaced */</span></div>
+<div class="line"><a name="l00344"></a><span class="lineno"> 344</span> \endverbatim</div>
+<div class="line"><a name="l00345"></a><span class="lineno"> 345</span> </div>
+<div class="line"><a name="l00346"></a><span class="lineno"> 346</span> The lower matrix uses the costs given in \cite shapiro:1990.</div>
+<div class="line"><a name="l00347"></a><span class="lineno"> 347</span> All distance functions use the following global variables:</div>
+<div class="line"><a name="l00348"></a><span class="lineno"> 348</span> </div>
+<div class="line"><a name="l00349"></a><span class="lineno"> 349</span> \verbatim</div>
+<div class="line"><a name="l00350"></a><span class="lineno"> 350</span> <span class="keywordtype">int</span> <a class="code" href="dist__vars_8h.html#ab65d8ff14c6937612212526a60f59b3c" title="Specify the cost matrix to be used for distance calculations.">cost_matrix</a>;</div>
+<div class="line"><a name="l00351"></a><span class="lineno"> 351</span> \endverbatim</div>
+<div class="line"><a name="l00352"></a><span class="lineno"> 352</span> \copybrief cost_matrix</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> \verbatim</div>
+<div class="line"><a name="l00355"></a><span class="lineno"> 355</span> <span class="keywordtype">int</span> <a class="code" href="dist__vars_8h.html#aa03194c513af6b860e7b33e370b82bdb" title="Produce an alignment of the two structures being compared by tracing the editing path giving the mini...">edit_backtrack</a>;</div>
+<div class="line"><a name="l00356"></a><span class="lineno"> 356</span> \endverbatim</div>
+<div class="line"><a name="l00357"></a><span class="lineno"> 357</span> \copybrief edit_backtrack</div>
+<div class="line"><a name="l00358"></a><span class="lineno"> 358</span> </div>
+<div class="line"><a name="l00359"></a><span class="lineno"> 359</span> \verbatim</div>
+<div class="line"><a name="l00360"></a><span class="lineno"> 360</span> <span class="keywordtype">char</span> *<a class="code" href="dist__vars_8h.html#ac1605fe3448ad0a0b809c4fb8f6a854a" title="Contains the two aligned structures after a call to one of the distance functions with edit_backtrack...">aligned_line</a>[4];</div>
+<div class="line"><a name="l00361"></a><span class="lineno"> 361</span> \endverbatim</div>
+<div class="line"><a name="l00362"></a><span class="lineno"> 362</span> \copybrief aligned_line</div>
+<div class="line"><a name="l00363"></a><span class="lineno"> 363</span> </div>
+<div class="line"><a name="l00364"></a><span class="lineno"> 364</span> \see utils.h, dist_vars.h and stringdist.h <span class="keywordflow">for</span> more details</div>
+<div class="line"><a name="l00365"></a><span class="lineno"> 365</span> </div>
+<div class="line"><a name="l00366"></a><span class="lineno"> 366</span> <h3>Functions <span class="keywordflow">for</span> <a class="code" href="structTree.html">Tree</a> Edit Distances</h3></div>
+<div class="line"><a name="l00367"></a><span class="lineno"> 367</span> </div>
+<div class="line"><a name="l00368"></a><span class="lineno"> 368</span> \verbatim</div>
+<div class="line"><a name="l00369"></a><span class="lineno"> 369</span> <a class="code" href="structTree.html">Tree</a> *<a class="code" href="treedist_8h.html#a08fe4d5afd385dce593b86eaf010c6e3" title="Constructs a Tree ( essentially the postorder list ) of the structure 'struc', for use in tree_edit_d...">make_tree</a> (<span class="keywordtype">char</span> *struc)</div>
+<div class="line"><a name="l00370"></a><span class="lineno"> 370</span> \endverbatim</div>
+<div class="line"><a name="l00371"></a><span class="lineno"> 371</span> \copybrief <a class="code" href="treedist_8h.html#a08fe4d5afd385dce593b86eaf010c6e3" title="Constructs a Tree ( essentially the postorder list ) of the structure 'struc', for use in tree_edit_d...">make_tree</a>()</div>
+<div class="line"><a name="l00372"></a><span class="lineno"> 372</span> </div>
+<div class="line"><a name="l00373"></a><span class="lineno"> 373</span> \verbatim</div>
+<div class="line"><a name="l00374"></a><span class="lineno"> 374</span> <span class="keywordtype">float</span> <a class="code" href="treedist_8h.html#a3b21f1925f7071f46d93431a835217bb" title="Calculates the edit distance of the two trees.">tree_edit_distance</a> (<a class="code" href="structTree.html">Tree</a> *T1,</div>
+<div class="line"><a name="l00375"></a><span class="lineno"> 375</span>  <a class="code" href="structTree.html">Tree</a> *T2) </div>
+<div class="line"><a name="l00376"></a><span class="lineno"> 376</span> \endverbatim</div>
+<div class="line"><a name="l00377"></a><span class="lineno"> 377</span> \copybrief <a class="code" href="treedist_8h.html#a3b21f1925f7071f46d93431a835217bb" title="Calculates the edit distance of the two trees.">tree_edit_distance</a>()</div>
+<div class="line"><a name="l00378"></a><span class="lineno"> 378</span> </div>
+<div class="line"><a name="l00379"></a><span class="lineno"> 379</span> \verbatim</div>
+<div class="line"><a name="l00380"></a><span class="lineno"> 380</span> <span class="keywordtype">void</span> <a class="code" href="treedist_8h.html#acbc1cb9bce582ea945e4a467c76a57aa" title="Free the memory allocated for Tree t.">free_tree</a>(<a class="code" href="structTree.html">Tree</a> *t)</div>
+<div class="line"><a name="l00381"></a><span class="lineno"> 381</span> \endverbatim</div>
+<div class="line"><a name="l00382"></a><span class="lineno"> 382</span> \copybrief <a class="code" href="treedist_8h.html#acbc1cb9bce582ea945e4a467c76a57aa" title="Free the memory allocated for Tree t.">free_tree</a>()</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> \see dist_vars.h and treedist.h <span class="keywordflow">for</span> prototypes and more detailed descriptions</div>
+<div class="line"><a name="l00385"></a><span class="lineno"> 385</span> </div>
+<div class="line"><a name="l00386"></a><span class="lineno"> 386</span> <h3>Functions <span class="keywordflow">for</span> String Alignment</h3></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> \verbatim</div>
+<div class="line"><a name="l00389"></a><span class="lineno"> 389</span> <a class="code" href="structswString.html">swString</a> *<a class="code" href="stringdist_8h.html#a3125991b3a403b3f89230474deb3f22e" title="Convert a structure into a format suitable for string_edit_distance().">Make_swString</a> (<span class="keywordtype">char</span> *<span class="keywordtype">string</span>)</div>
+<div class="line"><a name="l00390"></a><span class="lineno"> 390</span> \endverbatim</div>
+<div class="line"><a name="l00391"></a><span class="lineno"> 391</span> \copybrief <a class="code" href="stringdist_8h.html#a3125991b3a403b3f89230474deb3f22e" title="Convert a structure into a format suitable for string_edit_distance().">Make_swString</a>()</div>
+<div class="line"><a name="l00392"></a><span class="lineno"> 392</span> </div>
+<div class="line"><a name="l00393"></a><span class="lineno"> 393</span> \verbatim</div>
+<div class="line"><a name="l00394"></a><span class="lineno"> 394</span> <span class="keywordtype">float</span> <a class="code" href="stringdist_8h.html#a89e3c335ef17780576d7c0e713830db9" title="Calculate the string edit distance of T1 and T2.">string_edit_distance</a> (<a class="code" href="structswString.html">swString</a> *T1,</div>
+<div class="line"><a name="l00395"></a><span class="lineno"> 395</span>  <a class="code" href="structswString.html">swString</a> *T2)</div>
+<div class="line"><a name="l00396"></a><span class="lineno"> 396</span> \endverbatim</div>
+<div class="line"><a name="l00397"></a><span class="lineno"> 397</span> \copybrief <a class="code" href="stringdist_8h.html#a89e3c335ef17780576d7c0e713830db9" title="Calculate the string edit distance of T1 and T2.">string_edit_distance</a>()</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> \see dist_vars.h and stringdist.h <span class="keywordflow">for</span> prototypes and more detailed descriptions</div>
+<div class="line"><a name="l00400"></a><span class="lineno"> 400</span> </div>
+<div class="line"><a name="l00401"></a><span class="lineno"> 401</span> <h3>Functions <span class="keywordflow">for</span> Comparison of Base Pair Probabilities</h3></div>
+<div class="line"><a name="l00402"></a><span class="lineno"> 402</span> </div>
+<div class="line"><a name="l00403"></a><span class="lineno"> 403</span> For comparison of base pair probability matrices, the matrices are first</div>
+<div class="line"><a name="l00404"></a><span class="lineno"> 404</span> condensed into probability profiles which are the compared by alignment.</div>
+<div class="line"><a name="l00405"></a><span class="lineno"> 405</span> </div>
+<div class="line"><a name="l00406"></a><span class="lineno"> 406</span> \verbatim</div>
+<div class="line"><a name="l00407"></a><span class="lineno"> 407</span> <span class="keywordtype">float</span> *<a class="code" href="profiledist_8h.html#a8822fd5268be115c6e6cdc92009436cc" title="condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired.">Make_bp_profile_bppm</a> ( <span class="keywordtype">double</span> *bppm,</div>
+<div class="line"><a name="l00408"></a><span class="lineno"> 408</span>  <span class="keywordtype">int</span> length)</div>
+<div class="line"><a name="l00409"></a><span class="lineno"> 409</span> \endverbatim</div>
+<div class="line"><a name="l00410"></a><span class="lineno"> 410</span> \copybrief <a class="code" href="profiledist_8h.html#a8822fd5268be115c6e6cdc92009436cc" title="condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired.">Make_bp_profile_bppm</a>()</div>
+<div class="line"><a name="l00411"></a><span class="lineno"> 411</span> </div>
+<div class="line"><a name="l00412"></a><span class="lineno"> 412</span> \verbatim</div>
+<div class="line"><a name="l00413"></a><span class="lineno"> 413</span> <span class="keywordtype">float</span> <a class="code" href="profiledist_8h.html#abe75e90e00a1e5dd8862944ed53dad5d" title="Align the 2 probability profiles T1, T2 .">profile_edit_distance</a> ( <span class="keyword">const</span> <span class="keywordtype">float</span> *T1,</div>
+<div class="line"><a name="l00414"></a><span class="lineno"> 414</span>  <span class="keyword">const</span> <span class="keywordtype">float</span> *T2)</div>
+<div class="line"><a name="l00415"></a><span class="lineno"> 415</span> \endverbatim</div>
+<div class="line"><a name="l00416"></a><span class="lineno"> 416</span> \copybrief <a class="code" href="profiledist_8h.html#abe75e90e00a1e5dd8862944ed53dad5d" title="Align the 2 probability profiles T1, T2 .">profile_edit_distance</a>()</div>
+<div class="line"><a name="l00417"></a><span class="lineno"> 417</span> </div>
+<div class="line"><a name="l00418"></a><span class="lineno"> 418</span> \see ProfileDist.h <span class="keywordflow">for</span> prototypes and more details of the above functions</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> \ref mp_utils <span class="stringliteral">"Next Page: Utilities"</span></div>
+<div class="line"><a name="l00421"></a><span class="lineno"> 421</span> </div>
+<div class="line"><a name="l00422"></a><span class="lineno"> 422</span> \page mp_utils Utilities - Odds and Ends</div>
+<div class="line"><a name="l00423"></a><span class="lineno"> 423</span> </div>
+<div class="line"><a name="l00424"></a><span class="lineno"> 424</span> \anchor toc</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> <h3>Table of Contents</h3></div>
+<div class="line"><a name="l00427"></a><span class="lineno"> 427</span> <hr></div>
+<div class="line"><a name="l00428"></a><span class="lineno"> 428</span> </div>
+<div class="line"><a name="l00429"></a><span class="lineno"> 429</span> \li \ref utils_ss</div>
+<div class="line"><a name="l00430"></a><span class="lineno"> 430</span> \li \ref utils_dot</div>
+<div class="line"><a name="l00431"></a><span class="lineno"> 431</span> \li \ref utils_aln</div>
+<div class="line"><a name="l00432"></a><span class="lineno"> 432</span> \li \ref utils_seq</div>
+<div class="line"><a name="l00433"></a><span class="lineno"> 433</span> \li \ref utils_struc</div>
+<div class="line"><a name="l00434"></a><span class="lineno"> 434</span> \li \ref utils_misc</div>
+<div class="line"><a name="l00435"></a><span class="lineno"> 435</span> </div>
+<div class="line"><a name="l00436"></a><span class="lineno"> 436</span> <hr></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> \section utils_ss Producing secondary structure graphs</div>
+<div class="line"><a name="l00439"></a><span class="lineno"> 439</span> </div>
+<div class="line"><a name="l00440"></a><span class="lineno"> 440</span> \verbatim</div>
+<div class="line"><a name="l00441"></a><span class="lineno"> 441</span> <span class="keywordtype">int</span> <a class="code" href="PS__dot_8h.html#a0873c7cc4cd7a11c9a2cea19dde7e9c9" title="Produce a secondary structure graph in PostScript and write it to 'filename'.">PS_rna_plot</a> ( <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00442"></a><span class="lineno"> 442</span>  <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00443"></a><span class="lineno"> 443</span>  <span class="keywordtype">char</span> *file)</div>
+<div class="line"><a name="l00444"></a><span class="lineno"> 444</span> \endverbatim</div>
+<div class="line"><a name="l00445"></a><span class="lineno"> 445</span> \copybrief <a class="code" href="PS__dot_8h.html#a0873c7cc4cd7a11c9a2cea19dde7e9c9" title="Produce a secondary structure graph in PostScript and write it to 'filename'.">PS_rna_plot</a>()</div>
+<div class="line"><a name="l00446"></a><span class="lineno"> 446</span> </div>
+<div class="line"><a name="l00447"></a><span class="lineno"> 447</span> \verbatim</div>
+<div class="line"><a name="l00448"></a><span class="lineno"> 448</span> <span class="keywordtype">int</span> <a class="code" href="PS__dot_8h.html#a47856b2504b566588785597b6ebb8271" title="Produce a secondary structure graph in PostScript including additional annotation macros and write it...">PS_rna_plot_a</a> (</div>
+<div class="line"><a name="l00449"></a><span class="lineno"> 449</span>  <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00450"></a><span class="lineno"> 450</span>  <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00451"></a><span class="lineno"> 451</span>  <span class="keywordtype">char</span> *file,</div>
+<div class="line"><a name="l00452"></a><span class="lineno"> 452</span>  <span class="keywordtype">char</span> *pre,</div>
+<div class="line"><a name="l00453"></a><span class="lineno"> 453</span>  <span class="keywordtype">char</span> *post)</div>
+<div class="line"><a name="l00454"></a><span class="lineno"> 454</span> \endverbatim</div>
+<div class="line"><a name="l00455"></a><span class="lineno"> 455</span> \copybrief <a class="code" href="PS__dot_8h.html#a47856b2504b566588785597b6ebb8271" title="Produce a secondary structure graph in PostScript including additional annotation macros and write it...">PS_rna_plot_a</a>()</div>
+<div class="line"><a name="l00456"></a><span class="lineno"> 456</span> </div>
+<div class="line"><a name="l00457"></a><span class="lineno"> 457</span> \verbatim</div>
+<div class="line"><a name="l00458"></a><span class="lineno"> 458</span> <span class="keywordtype">int</span> <a class="code" href="PS__dot_8h.html#a70834bc8c0aad4fe6824ff76ccb8f329" title="Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file...">gmlRNA</a> (<span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00459"></a><span class="lineno"> 459</span>  <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00460"></a><span class="lineno"> 460</span>  <span class="keywordtype">char</span> *ssfile,</div>
+<div class="line"><a name="l00461"></a><span class="lineno"> 461</span>  <span class="keywordtype">char</span> option)</div>
+<div class="line"><a name="l00462"></a><span class="lineno"> 462</span> \endverbatim</div>
+<div class="line"><a name="l00463"></a><span class="lineno"> 463</span> \copybrief <a class="code" href="PS__dot_8h.html#a70834bc8c0aad4fe6824ff76ccb8f329" title="Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file...">gmlRNA</a>()</div>
+<div class="line"><a name="l00464"></a><span class="lineno"> 464</span> </div>
+<div class="line"><a name="l00465"></a><span class="lineno"> 465</span> \verbatim</div>
+<div class="line"><a name="l00466"></a><span class="lineno"> 466</span> <span class="keywordtype">int</span> <a class="code" href="PS__dot_8h.html#add368528755f9a830727b680243541df" title="Produce a secondary structure graph in SStructView format.">ssv_rna_plot</a> (<span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00467"></a><span class="lineno"> 467</span>  <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00468"></a><span class="lineno"> 468</span>  <span class="keywordtype">char</span> *ssfile)</div>
+<div class="line"><a name="l00469"></a><span class="lineno"> 469</span> \endverbatim</div>
+<div class="line"><a name="l00470"></a><span class="lineno"> 470</span> \copybrief <a class="code" href="PS__dot_8h.html#add368528755f9a830727b680243541df" title="Produce a secondary structure graph in SStructView format.">ssv_rna_plot</a>()</div>
+<div class="line"><a name="l00471"></a><span class="lineno"> 471</span> </div>
+<div class="line"><a name="l00472"></a><span class="lineno"> 472</span> \verbatim</div>
+<div class="line"><a name="l00473"></a><span class="lineno"> 473</span> <span class="keywordtype">int</span> <a class="code" href="PS__dot_8h.html#ae7853539b5df98f294b4af434e979304" title="Produce a secondary structure plot in SVG format and write it to a file.">svg_rna_plot</a> (<span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00474"></a><span class="lineno"> 474</span>  <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00475"></a><span class="lineno"> 475</span>  <span class="keywordtype">char</span> *ssfile)</div>
+<div class="line"><a name="l00476"></a><span class="lineno"> 476</span> \endverbatim</div>
+<div class="line"><a name="l00477"></a><span class="lineno"> 477</span> \copybrief <a class="code" href="PS__dot_8h.html#ae7853539b5df98f294b4af434e979304" title="Produce a secondary structure plot in SVG format and write it to a file.">svg_rna_plot</a>()</div>
+<div class="line"><a name="l00478"></a><span class="lineno"> 478</span> </div>
+<div class="line"><a name="l00479"></a><span class="lineno"> 479</span> \verbatim</div>
+<div class="line"><a name="l00480"></a><span class="lineno"> 480</span> <span class="keywordtype">int</span> <a class="code" href="PS__dot_8h.html#a2f6d5953e6a323df898896b8d6614483" title="Produce a secondary structure plot for further editing in XRNA.">xrna_plot</a> ( <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00481"></a><span class="lineno"> 481</span>  <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00482"></a><span class="lineno"> 482</span>  <span class="keywordtype">char</span> *ssfile)</div>
+<div class="line"><a name="l00483"></a><span class="lineno"> 483</span> \endverbatim</div>
+<div class="line"><a name="l00484"></a><span class="lineno"> 484</span> \copybrief <a class="code" href="PS__dot_8h.html#a2f6d5953e6a323df898896b8d6614483" title="Produce a secondary structure plot for further editing in XRNA.">xrna_plot</a>()</div>
+<div class="line"><a name="l00485"></a><span class="lineno"> 485</span> </div>
+<div class="line"><a name="l00486"></a><span class="lineno"> 486</span> \verbatim</div>
+<div class="line"><a name="l00487"></a><span class="lineno"> 487</span> <span class="keywordtype">int</span> rna_plot_type</div>
+<div class="line"><a name="l00488"></a><span class="lineno"> 488</span> \endverbatim</div>
+<div class="line"><a name="l00489"></a><span class="lineno"> 489</span> \copybrief <a class="code" href="plot__layouts_8h.html#a5964c4581431b098b80027d6e14dcdd4" title="Switch for changing the secondary structure layout algorithm.">rna_plot_type</a></div>
+<div class="line"><a name="l00490"></a><span class="lineno"> 490</span> </div>
+<div class="line"><a name="l00491"></a><span class="lineno"> 491</span> Two low-level functions provide direct access to the graph lauyouting</div>
+<div class="line"><a name="l00492"></a><span class="lineno"> 492</span> algorithms:</div>
+<div class="line"><a name="l00493"></a><span class="lineno"> 493</span> </div>
+<div class="line"><a name="l00494"></a><span class="lineno"> 494</span> \verbatim</div>
+<div class="line"><a name="l00495"></a><span class="lineno"> 495</span> <span class="keywordtype">int</span> <a class="code" href="plot__layouts_8h.html#af4b9173e7d3fd361c3c85e6def194123" title="Calculate nucleotide coordinates for secondary structure plot the Simple way">simple_xy_coordinates</a> ( <span class="keywordtype">short</span> *pair_table,</div>
+<div class="line"><a name="l00496"></a><span class="lineno"> 496</span>  <span class="keywordtype">float</span> *X,</div>
+<div class="line"><a name="l00497"></a><span class="lineno"> 497</span>  <span class="keywordtype">float</span> *Y)</div>
+<div class="line"><a name="l00498"></a><span class="lineno"> 498</span> \endverbatim</div>
+<div class="line"><a name="l00499"></a><span class="lineno"> 499</span> \copybrief <a class="code" href="plot__layouts_8h.html#af4b9173e7d3fd361c3c85e6def194123" title="Calculate nucleotide coordinates for secondary structure plot the Simple way">simple_xy_coordinates</a>()</div>
+<div class="line"><a name="l00500"></a><span class="lineno"> 500</span> </div>
+<div class="line"><a name="l00501"></a><span class="lineno"> 501</span> \verbatim</div>
+<div class="line"><a name="l00502"></a><span class="lineno"> 502</span> <span class="keywordtype">int</span> naview_xy_coordinates ( <span class="keywordtype">short</span> *pair_table,</div>
+<div class="line"><a name="l00503"></a><span class="lineno"> 503</span>  <span class="keywordtype">float</span> *X,</div>
+<div class="line"><a name="l00504"></a><span class="lineno"> 504</span>  <span class="keywordtype">float</span> *Y)</div>
+<div class="line"><a name="l00505"></a><span class="lineno"> 505</span> \endverbatim</div>
+<div class="line"><a name="l00506"></a><span class="lineno"> 506</span> \copybrief naview_xy_coordinates()</div>
+<div class="line"><a name="l00507"></a><span class="lineno"> 507</span> </div>
+<div class="line"><a name="l00508"></a><span class="lineno"> 508</span> \see PS_dot.h and naview.h <span class="keywordflow">for</span> more detailed descriptions.</div>
+<div class="line"><a name="l00509"></a><span class="lineno"> 509</span> </div>
+<div class="line"><a name="l00510"></a><span class="lineno"> 510</span> \htmlonly</div>
+<div class="line"><a name="l00511"></a><span class="lineno"> 511</span> <hr></div>
+<div class="line"><a name="l00512"></a><span class="lineno"> 512</span> <a href=<span class="stringliteral">"#toc"</span>>Table of Contents</a></div>
+<div class="line"><a name="l00513"></a><span class="lineno"> 513</span> <hr></div>
+<div class="line"><a name="l00514"></a><span class="lineno"> 514</span> \endhtmlonly</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> \section utils_dot Producing (colored) dot plots for base pair probabilities</div>
+<div class="line"><a name="l00517"></a><span class="lineno"> 517</span> </div>
+<div class="line"><a name="l00518"></a><span class="lineno"> 518</span> \verbatim</div>
+<div class="line"><a name="l00519"></a><span class="lineno"> 519</span> <span class="keywordtype">int</span> PS_color_dot_plot ( <span class="keywordtype">char</span> *<span class="keywordtype">string</span>,</div>
+<div class="line"><a name="l00520"></a><span class="lineno"> 520</span>  <a class="code" href="structcpair.html" title="this datastructure is used as input parameter in functions of PS_dot.c">cpair</a> *pi,</div>
+<div class="line"><a name="l00521"></a><span class="lineno"> 521</span>  <span class="keywordtype">char</span> *filename)</div>
+<div class="line"><a name="l00522"></a><span class="lineno"> 522</span> \endverbatim</div>
+<div class="line"><a name="l00523"></a><span class="lineno"> 523</span> \copybrief PS_color_dot_plot()</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> \verbatim</div>
+<div class="line"><a name="l00526"></a><span class="lineno"> 526</span> <span class="keywordtype">int</span> PS_color_dot_plot_turn (<span class="keywordtype">char</span> *seq,</div>
+<div class="line"><a name="l00527"></a><span class="lineno"> 527</span>  <a class="code" href="structcpair.html" title="this datastructure is used as input parameter in functions of PS_dot.c">cpair</a> *pi,</div>
+<div class="line"><a name="l00528"></a><span class="lineno"> 528</span>  <span class="keywordtype">char</span> *filename,</div>
+<div class="line"><a name="l00529"></a><span class="lineno"> 529</span>  <span class="keywordtype">int</span> winSize)</div>
+<div class="line"><a name="l00530"></a><span class="lineno"> 530</span> \endverbatim</div>
+<div class="line"><a name="l00531"></a><span class="lineno"> 531</span> \copybrief PS_color_dot_plot_turn()</div>
+<div class="line"><a name="l00532"></a><span class="lineno"> 532</span> </div>
+<div class="line"><a name="l00533"></a><span class="lineno"> 533</span> \verbatim</div>
+<div class="line"><a name="l00534"></a><span class="lineno"> 534</span> <span class="keywordtype">int</span> <a class="code" href="PS__dot_8h.html#a00ea223b5cf02eb2faae5ff29f0d5e12" title="Produce a postscript dot-plot from two pair lists.">PS_dot_plot_list</a> (<span class="keywordtype">char</span> *seq,</div>
+<div class="line"><a name="l00535"></a><span class="lineno"> 535</span>  <span class="keywordtype">char</span> *filename,</div>
+<div class="line"><a name="l00536"></a><span class="lineno"> 536</span>  <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *pl,</div>
+<div class="line"><a name="l00537"></a><span class="lineno"> 537</span>  <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *mf,</div>
+<div class="line"><a name="l00538"></a><span class="lineno"> 538</span>  <span class="keywordtype">char</span> *comment)</div>
+<div class="line"><a name="l00539"></a><span class="lineno"> 539</span> \endverbatim</div>
+<div class="line"><a name="l00540"></a><span class="lineno"> 540</span> \copybrief <a class="code" href="PS__dot_8h.html#a00ea223b5cf02eb2faae5ff29f0d5e12" title="Produce a postscript dot-plot from two pair lists.">PS_dot_plot_list</a>()</div>
+<div class="line"><a name="l00541"></a><span class="lineno"> 541</span> </div>
+<div class="line"><a name="l00542"></a><span class="lineno"> 542</span> \verbatim</div>
+<div class="line"><a name="l00543"></a><span class="lineno"> 543</span> <span class="keywordtype">int</span> PS_dot_plot_turn (<span class="keywordtype">char</span> *seq,</div>
+<div class="line"><a name="l00544"></a><span class="lineno"> 544</span>  struct <a class="code" href="structplist.html" title="this datastructure is used as input parameter in functions of PS_dot.h and others">plist</a> *pl,</div>
+<div class="line"><a name="l00545"></a><span class="lineno"> 545</span>  <span class="keywordtype">char</span> *filename,</div>
+<div class="line"><a name="l00546"></a><span class="lineno"> 546</span>  <span class="keywordtype">int</span> winSize)</div>
+<div class="line"><a name="l00547"></a><span class="lineno"> 547</span> \endverbatim</div>
+<div class="line"><a name="l00548"></a><span class="lineno"> 548</span> \copybrief PS_dot_plot_turn()</div>
+<div class="line"><a name="l00549"></a><span class="lineno"> 549</span> </div>
+<div class="line"><a name="l00550"></a><span class="lineno"> 550</span> \see PS_dot.h for more detailed descriptions.</div>
+<div class="line"><a name="l00551"></a><span class="lineno"> 551</span> </div>
+<div class="line"><a name="l00552"></a><span class="lineno"> 552</span> \section utils_aln Producing (colored) alignments</div>
+<div class="line"><a name="l00553"></a><span class="lineno"> 553</span> </div>
+<div class="line"><a name="l00554"></a><span class="lineno"> 554</span> \verbatim</div>
+<div class="line"><a name="l00555"></a><span class="lineno"> 555</span> <span class="keywordtype">int</span> PS_color_aln (</div>
+<div class="line"><a name="l00556"></a><span class="lineno"> 556</span>  const <span class="keywordtype">char</span> *structure,</div>
+<div class="line"><a name="l00557"></a><span class="lineno"> 557</span>  const <span class="keywordtype">char</span> *filename,</div>
+<div class="line"><a name="l00558"></a><span class="lineno"> 558</span>  const <span class="keywordtype">char</span> *seqs[],</div>
+<div class="line"><a name="l00559"></a><span class="lineno"> 559</span>  const <span class="keywordtype">char</span> *names[])</div>
+<div class="line"><a name="l00560"></a><span class="lineno"> 560</span> \endverbatim</div>
+<div class="line"><a name="l00561"></a><span class="lineno"> 561</span> \copybrief PS_color_aln()</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> \htmlonly</div>
+<div class="line"><a name="l00564"></a><span class="lineno"> 564</span> <hr></div>
+<div class="line"><a name="l00565"></a><span class="lineno"> 565</span> <a href="<span class="preprocessor">#toc">Table of Contents</a></span></div>
+<div class="line"><a name="l00566"></a><span class="lineno"> 566</span> <span class="preprocessor"></span><hr></div>
+<div class="line"><a name="l00567"></a><span class="lineno"> 567</span> \endhtmlonly</div>
+<div class="line"><a name="l00568"></a><span class="lineno"> 568</span> </div>
+<div class="line"><a name="l00569"></a><span class="lineno"> 569</span> \section utils_seq RNA sequence related utilities</div>
+<div class="line"><a name="l00570"></a><span class="lineno"> 570</span> </div>
+<div class="line"><a name="l00571"></a><span class="lineno"> 571</span> Several functions provide useful applications to RNA sequences</div>
+<div class="line"><a name="l00572"></a><span class="lineno"> 572</span> </div>
+<div class="line"><a name="l00573"></a><span class="lineno"> 573</span> \verbatim</div>
+<div class="line"><a name="l00574"></a><span class="lineno"> 574</span> <span class="keywordtype">char</span> *<a class="code" href="utils_8h.html#a1b95eac365a021572e1c37e5993a89be" title="Create a random string using characters from a specified symbol set.">random_string</a> (<span class="keywordtype">int</span> l,</div>
+<div class="line"><a name="l00575"></a><span class="lineno"> 575</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> symbols[])</div>
+<div class="line"><a name="l00576"></a><span class="lineno"> 576</span> \endverbatim</div>
+<div class="line"><a name="l00577"></a><span class="lineno"> 577</span> \copybrief <a class="code" href="utils_8h.html#a1b95eac365a021572e1c37e5993a89be" title="Create a random string using characters from a specified symbol set.">random_string</a>()</div>
+<div class="line"><a name="l00578"></a><span class="lineno"> 578</span> </div>
+<div class="line"><a name="l00579"></a><span class="lineno"> 579</span> \verbatim</div>
+<div class="line"><a name="l00580"></a><span class="lineno"> 580</span> <span class="keywordtype">int</span> <a class="code" href="utils_8h.html#ad9dc7bfc9aa664dc6698f17ce07fc7e7" title="Calculate hamming distance between two sequences.">hamming</a> ( <span class="keyword">const</span> <span class="keywordtype">char</span> *s1,</div>
+<div class="line"><a name="l00581"></a><span class="lineno"> 581</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *s2)</div>
+<div class="line"><a name="l00582"></a><span class="lineno"> 582</span> \endverbatim</div>
+<div class="line"><a name="l00583"></a><span class="lineno"> 583</span> \copybrief <a class="code" href="utils_8h.html#ad9dc7bfc9aa664dc6698f17ce07fc7e7" title="Calculate hamming distance between two sequences.">hamming</a>()</div>
+<div class="line"><a name="l00584"></a><span class="lineno"> 584</span> </div>
+<div class="line"><a name="l00585"></a><span class="lineno"> 585</span> \verbatim</div>
+<div class="line"><a name="l00586"></a><span class="lineno"> 586</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#ad3f18dd83f958f18b2f26ecb99305208" title="Convert a DNA input sequence to RNA alphabet.">str_DNA2RNA</a>(<span class="keywordtype">char</span> *sequence);</div>
+<div class="line"><a name="l00587"></a><span class="lineno"> 587</span> \endverbatim</div>
+<div class="line"><a name="l00588"></a><span class="lineno"> 588</span> \copybrief <a class="code" href="utils_8h.html#ad3f18dd83f958f18b2f26ecb99305208" title="Convert a DNA input sequence to RNA alphabet.">str_DNA2RNA</a>()</div>
+<div class="line"><a name="l00589"></a><span class="lineno"> 589</span> </div>
+<div class="line"><a name="l00590"></a><span class="lineno"> 590</span> \verbatim</div>
+<div class="line"><a name="l00591"></a><span class="lineno"> 591</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#a17b796b806f96b70382077fb5bc519bb" title="Convert an input sequence to uppercase.">str_uppercase</a>(<span class="keywordtype">char</span> *sequence);</div>
+<div class="line"><a name="l00592"></a><span class="lineno"> 592</span> \endverbatim</div>
+<div class="line"><a name="l00593"></a><span class="lineno"> 593</span> \copybrief <a class="code" href="utils_8h.html#a17b796b806f96b70382077fb5bc519bb" title="Convert an input sequence to uppercase.">str_uppercase</a>()</div>
+<div class="line"><a name="l00594"></a><span class="lineno"> 594</span> </div>
+<div class="line"><a name="l00595"></a><span class="lineno"> 595</span> \htmlonly</div>
+<div class="line"><a name="l00596"></a><span class="lineno"> 596</span> <hr></div>
+<div class="line"><a name="l00597"></a><span class="lineno"> 597</span> <a href=<span class="stringliteral">"#toc"</span>>Table of Contents</a></div>
+<div class="line"><a name="l00598"></a><span class="lineno"> 598</span> <hr></div>
+<div class="line"><a name="l00599"></a><span class="lineno"> 599</span> \endhtmlonly</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> \section utils_struc RNA secondary structure related utilities</div>
+<div class="line"><a name="l00602"></a><span class="lineno"> 602</span> </div>
+<div class="line"><a name="l00603"></a><span class="lineno"> 603</span> \verbatim</div>
+<div class="line"><a name="l00604"></a><span class="lineno"> 604</span> <span class="keywordtype">char</span> *<a class="code" href="utils_8h.html#ac6dfa5e22928c087c6e09ff0054a7ced" title="Pack secondary secondary structure, 5:1 compression using base 3 encoding.">pack_structure</a> (<span class="keyword">const</span> <span class="keywordtype">char</span> *struc)</div>
+<div class="line"><a name="l00605"></a><span class="lineno"> 605</span> \endverbatim</div>
+<div class="line"><a name="l00606"></a><span class="lineno"> 606</span> \copybrief <a class="code" href="utils_8h.html#ac6dfa5e22928c087c6e09ff0054a7ced" title="Pack secondary secondary structure, 5:1 compression using base 3 encoding.">pack_structure</a>()</div>
+<div class="line"><a name="l00607"></a><span class="lineno"> 607</span> </div>
+<div class="line"><a name="l00608"></a><span class="lineno"> 608</span> \verbatim</div>
+<div class="line"><a name="l00609"></a><span class="lineno"> 609</span> <span class="keywordtype">char</span> *<a class="code" href="utils_8h.html#a071c6921efe1eb974f115ee6fefa3c39" title="Unpack secondary structure previously packed with pack_structure()">unpack_structure</a> (<span class="keyword">const</span> <span class="keywordtype">char</span> *packed)</div>
+<div class="line"><a name="l00610"></a><span class="lineno"> 610</span> \endverbatim</div>
+<div class="line"><a name="l00611"></a><span class="lineno"> 611</span> \copybrief <a class="code" href="utils_8h.html#a071c6921efe1eb974f115ee6fefa3c39" title="Unpack secondary structure previously packed with pack_structure()">unpack_structure</a>()</div>
+<div class="line"><a name="l00612"></a><span class="lineno"> 612</span> </div>
+<div class="line"><a name="l00613"></a><span class="lineno"> 613</span> \verbatim</div>
+<div class="line"><a name="l00614"></a><span class="lineno"> 614</span> <span class="keywordtype">short</span> *<a class="code" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a" title="Create a pair table of a secondary structure.">make_pair_table</a> (<span class="keyword">const</span> <span class="keywordtype">char</span> *structure)</div>
+<div class="line"><a name="l00615"></a><span class="lineno"> 615</span> \endverbatim</div>
+<div class="line"><a name="l00616"></a><span class="lineno"> 616</span> \copybrief <a class="code" href="utils_8h.html#a89c32307ee50a0026f4a3131fac0845a" title="Create a pair table of a secondary structure.">make_pair_table</a>()</div>
+<div class="line"><a name="l00617"></a><span class="lineno"> 617</span> </div>
+<div class="line"><a name="l00618"></a><span class="lineno"> 618</span> \verbatim</div>
+<div class="line"><a name="l00619"></a><span class="lineno"> 619</span> <span class="keywordtype">short</span> *<a class="code" href="utils_8h.html#afeaa6d68eef3a99d0a7aa08aa91c6601" title="Get an exact copy of a pair table.">copy_pair_table</a> (<span class="keyword">const</span> <span class="keywordtype">short</span> *pt)</div>
+<div class="line"><a name="l00620"></a><span class="lineno"> 620</span> \endverbatim</div>
+<div class="line"><a name="l00621"></a><span class="lineno"> 621</span> \copybrief <a class="code" href="utils_8h.html#afeaa6d68eef3a99d0a7aa08aa91c6601" title="Get an exact copy of a pair table.">copy_pair_table</a>()</div>
+<div class="line"><a name="l00622"></a><span class="lineno"> 622</span> </div>
+<div class="line"><a name="l00623"></a><span class="lineno"> 623</span> \htmlonly</div>
+<div class="line"><a name="l00624"></a><span class="lineno"> 624</span> <hr></div>
+<div class="line"><a name="l00625"></a><span class="lineno"> 625</span> <a href=<span class="stringliteral">"#toc"</span>>Table of Contents</a></div>
+<div class="line"><a name="l00626"></a><span class="lineno"> 626</span> <hr></div>
+<div class="line"><a name="l00627"></a><span class="lineno"> 627</span> \endhtmlonly</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> \section utils_misc Miscellaneous Utilities</div>
+<div class="line"><a name="l00630"></a><span class="lineno"> 630</span> </div>
+<div class="line"><a name="l00631"></a><span class="lineno"> 631</span> \verbatim</div>
+<div class="line"><a name="l00632"></a><span class="lineno"> 632</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#a6bf778117d31b7fd90db435323f4ef74" title="Print a line to stdout that asks for an input sequence.">print_tty_input_seq</a> (<span class="keywordtype">void</span>)</div>
+<div class="line"><a name="l00633"></a><span class="lineno"> 633</span> \endverbatim</div>
+<div class="line"><a name="l00634"></a><span class="lineno"> 634</span> \copybrief <a class="code" href="utils_8h.html#a6bf778117d31b7fd90db435323f4ef74" title="Print a line to stdout that asks for an input sequence.">print_tty_input_seq</a>()</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> \verbatim</div>
+<div class="line"><a name="l00637"></a><span class="lineno"> 637</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#ae8ae8a34962b9959be3f6c40f0a80ac1" title="Print structure constraint characters to stdout (full constraint support)">print_tty_constraint_full</a> (<span class="keywordtype">void</span>)</div>
+<div class="line"><a name="l00638"></a><span class="lineno"> 638</span> \endverbatim</div>
+<div class="line"><a name="l00639"></a><span class="lineno"> 639</span> \copybrief <a class="code" href="utils_8h.html#ae8ae8a34962b9959be3f6c40f0a80ac1" title="Print structure constraint characters to stdout (full constraint support)">print_tty_constraint_full</a>()</div>
+<div class="line"><a name="l00640"></a><span class="lineno"> 640</span> </div>
+<div class="line"><a name="l00641"></a><span class="lineno"> 641</span> \verbatim</div>
+<div class="line"><a name="l00642"></a><span class="lineno"> 642</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#a4d167deb70bb51723e44374dc981deb2" title="Print structure constraint characters to stdout. (constraint support is specified by option parameter...">print_tty_constraint</a> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> option)</div>
+<div class="line"><a name="l00643"></a><span class="lineno"> 643</span> \endverbatim</div>
+<div class="line"><a name="l00644"></a><span class="lineno"> 644</span> \copybrief <a class="code" href="utils_8h.html#a4d167deb70bb51723e44374dc981deb2" title="Print structure constraint characters to stdout. (constraint support is specified by option parameter...">print_tty_constraint</a>()</div>
+<div class="line"><a name="l00645"></a><span class="lineno"> 645</span> </div>
+<div class="line"><a name="l00646"></a><span class="lineno"> 646</span> \verbatim</div>
+<div class="line"><a name="l00647"></a><span class="lineno"> 647</span> <span class="keywordtype">int</span> *<a class="code" href="utils_8h.html#a55c0f6b3b07b6adf2ee235ba901fe397" title="Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function relat...">get_iindx</a> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> length)</div>
+<div class="line"><a name="l00648"></a><span class="lineno"> 648</span> \endverbatim</div>
+<div class="line"><a name="l00649"></a><span class="lineno"> 649</span> \copybrief <a class="code" href="utils_8h.html#a55c0f6b3b07b6adf2ee235ba901fe397" title="Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function relat...">get_iindx</a>()</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> \verbatim</div>
+<div class="line"><a name="l00652"></a><span class="lineno"> 652</span> <span class="keywordtype">int</span> *<a class="code" href="utils_8h.html#a4d9ee1572c1bfcd02d3d3f2db8a6530f" title="Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions...">get_indx</a> (<span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> length)</div>
+<div class="line"><a name="l00653"></a><span class="lineno"> 653</span> \endverbatim</div>
+<div class="line"><a name="l00654"></a><span class="lineno"> 654</span> \copybrief <a class="code" href="utils_8h.html#a4d9ee1572c1bfcd02d3d3f2db8a6530f" title="Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions...">get_indx</a>()</div>
+<div class="line"><a name="l00655"></a><span class="lineno"> 655</span> </div>
+<div class="line"><a name="l00656"></a><span class="lineno"> 656</span> \verbatim</div>
+<div class="line"><a name="l00657"></a><span class="lineno"> 657</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#a36c3a6c3218b041f992052767bc74549" title="Insert constraining pair types according to constraint structure string.">constrain_ptypes</a> (</div>
+<div class="line"><a name="l00658"></a><span class="lineno"> 658</span>  <span class="keyword">const</span> <span class="keywordtype">char</span> *constraint,</div>
+<div class="line"><a name="l00659"></a><span class="lineno"> 659</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> length,</div>
+<div class="line"><a name="l00660"></a><span class="lineno"> 660</span>  <span class="keywordtype">char</span> *ptype,</div>
+<div class="line"><a name="l00661"></a><span class="lineno"> 661</span>  <span class="keywordtype">int</span> *BP,</div>
+<div class="line"><a name="l00662"></a><span class="lineno"> 662</span>  <span class="keywordtype">int</span> min_loop_size,</div>
+<div class="line"><a name="l00663"></a><span class="lineno"> 663</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> idx_type)</div>
+<div class="line"><a name="l00664"></a><span class="lineno"> 664</span> \endverbatim</div>
+<div class="line"><a name="l00665"></a><span class="lineno"> 665</span> \copybrief <a class="code" href="utils_8h.html#a36c3a6c3218b041f992052767bc74549" title="Insert constraining pair types according to constraint structure string.">constrain_ptypes</a>()</div>
+<div class="line"><a name="l00666"></a><span class="lineno"> 666</span> </div>
+<div class="line"><a name="l00667"></a><span class="lineno"> 667</span> \verbatim</div>
+<div class="line"><a name="l00668"></a><span class="lineno"> 668</span> <span class="keywordtype">char</span> *<a class="code" href="utils_8h.html#abe51806d14cff0789a8c1df7dbc45b71" title="Read a line of arbitrary length from a stream.">get_line</a>(FILE *fp);</div>
+<div class="line"><a name="l00669"></a><span class="lineno"> 669</span> \endverbatim</div>
+<div class="line"><a name="l00670"></a><span class="lineno"> 670</span> \copybrief <a class="code" href="utils_8h.html#abe51806d14cff0789a8c1df7dbc45b71" title="Read a line of arbitrary length from a stream.">get_line</a>()</div>
+<div class="line"><a name="l00671"></a><span class="lineno"> 671</span> </div>
+<div class="line"><a name="l00672"></a><span class="lineno"> 672</span> \verbatim</div>
+<div class="line"><a name="l00673"></a><span class="lineno"> 673</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> <a class="code" href="utils_8h.html#afd194a69af9d92b5b0412a7627ac1595" title="Get a data record from stdin.">read_record</a>(</div>
+<div class="line"><a name="l00674"></a><span class="lineno"> 674</span>  <span class="keywordtype">char</span> **header,</div>
+<div class="line"><a name="l00675"></a><span class="lineno"> 675</span>  <span class="keywordtype">char</span> **sequence,</div>
+<div class="line"><a name="l00676"></a><span class="lineno"> 676</span>  <span class="keywordtype">char</span> ***rest,</div>
+<div class="line"><a name="l00677"></a><span class="lineno"> 677</span>  <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span> options);</div>
+<div class="line"><a name="l00678"></a><span class="lineno"> 678</span> \endverbatim</div>
+<div class="line"><a name="l00679"></a><span class="lineno"> 679</span> \copybrief <a class="code" href="utils_8h.html#afd194a69af9d92b5b0412a7627ac1595" title="Get a data record from stdin.">read_record</a>()</div>
+<div class="line"><a name="l00680"></a><span class="lineno"> 680</span> </div>
+<div class="line"><a name="l00681"></a><span class="lineno"> 681</span> \verbatim</div>
+<div class="line"><a name="l00682"></a><span class="lineno"> 682</span> <span class="keywordtype">char</span> *<a class="code" href="utils_8h.html#a7afeb906cb36e9d77379eabc6907ac46" title="Get a timestamp.">time_stamp</a> (<span class="keywordtype">void</span>)</div>
+<div class="line"><a name="l00683"></a><span class="lineno"> 683</span> \endverbatim</div>
+<div class="line"><a name="l00684"></a><span class="lineno"> 684</span> \copybrief <a class="code" href="utils_8h.html#a7afeb906cb36e9d77379eabc6907ac46" title="Get a timestamp.">time_stamp</a>()</div>
+<div class="line"><a name="l00685"></a><span class="lineno"> 685</span> </div>
+<div class="line"><a name="l00686"></a><span class="lineno"> 686</span> \verbatim</div>
+<div class="line"><a name="l00687"></a><span class="lineno"> 687</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#af2355fa8746f2f30fbe71db65dea3d51" title="Print a warning message.">warn_user</a> (<span class="keyword">const</span> <span class="keywordtype">char</span> message[])</div>
+<div class="line"><a name="l00688"></a><span class="lineno"> 688</span> \endverbatim</div>
+<div class="line"><a name="l00689"></a><span class="lineno"> 689</span> \copybrief <a class="code" href="utils_8h.html#af2355fa8746f2f30fbe71db65dea3d51" title="Print a warning message.">warn_user</a>()</div>
+<div class="line"><a name="l00690"></a><span class="lineno"> 690</span> </div>
+<div class="line"><a name="l00691"></a><span class="lineno"> 691</span> \verbatim</div>
+<div class="line"><a name="l00692"></a><span class="lineno"> 692</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#a127ce946e56b5a5773781cabe68e38c5" title="Die with an error message.">nrerror</a> (<span class="keyword">const</span> <span class="keywordtype">char</span> message[])</div>
+<div class="line"><a name="l00693"></a><span class="lineno"> 693</span> \endverbatim</div>
+<div class="line"><a name="l00694"></a><span class="lineno"> 694</span> \copybrief <a class="code" href="utils_8h.html#a127ce946e56b5a5773781cabe68e38c5" title="Die with an error message.">nrerror</a>()</div>
+<div class="line"><a name="l00695"></a><span class="lineno"> 695</span> </div>
+<div class="line"><a name="l00696"></a><span class="lineno"> 696</span> \verbatim</div>
+<div class="line"><a name="l00697"></a><span class="lineno"> 697</span> <span class="keywordtype">void</span> <a class="code" href="utils_8h.html#a8aaa6d9be6f803f496d9b97375c371f3" title="Make random number seeds.">init_rand</a> (<span class="keywordtype">void</span>)</div>
+<div class="line"><a name="l00698"></a><span class="lineno"> 698</span> \endverbatim</div>
+<div class="line"><a name="l00699"></a><span class="lineno"> 699</span> \copybrief <a class="code" href="utils_8h.html#a8aaa6d9be6f803f496d9b97375c371f3" title="Make random number seeds.">init_rand</a>()</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> \verbatim</div>
+<div class="line"><a name="l00702"></a><span class="lineno"> 702</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span> <a class="code" href="utils_8h.html#af9a866c8417afda7368bbac939ab3c47" title="Current 48 bit random number.">xsubi</a>[3];</div>
+<div class="line"><a name="l00703"></a><span class="lineno"> 703</span> \endverbatim</div>
+<div class="line"><a name="l00704"></a><span class="lineno"> 704</span> \copybrief xsubi</div>
+<div class="line"><a name="l00705"></a><span class="lineno"> 705</span> </div>
+<div class="line"><a name="l00706"></a><span class="lineno"> 706</span> \verbatim</div>
+<div class="line"><a name="l00707"></a><span class="lineno"> 707</span> <span class="keywordtype">double</span> <a class="code" href="utils_8h.html#aaa328491c84996e445d027fde9800f2e" title="get a random number from [0..1]">urn</a> (<span class="keywordtype">void</span>)</div>
+<div class="line"><a name="l00708"></a><span class="lineno"> 708</span> \endverbatim</div>
+<div class="line"><a name="l00709"></a><span class="lineno"> 709</span> \copybrief <a class="code" href="utils_8h.html#aaa328491c84996e445d027fde9800f2e" title="get a random number from [0..1]">urn</a>()</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> \verbatim</div>
+<div class="line"><a name="l00712"></a><span class="lineno"> 712</span> <span class="keywordtype">int</span> <a class="code" href="utils_8h.html#a68ff0849d44f62fe491800378a5ffcb4" title="Generates a pseudo random integer in a specified range.">int_urn</a> (<span class="keywordtype">int</span> from, <span class="keywordtype">int</span> to)</div>
+<div class="line"><a name="l00713"></a><span class="lineno"> 713</span> \endverbatim</div>
+<div class="line"><a name="l00714"></a><span class="lineno"> 714</span> \copybrief <a class="code" href="utils_8h.html#a68ff0849d44f62fe491800378a5ffcb4" title="Generates a pseudo random integer in a specified range.">int_urn</a>()</div>
+<div class="line"><a name="l00715"></a><span class="lineno"> 715</span> </div>
+<div class="line"><a name="l00716"></a><span class="lineno"> 716</span> \verbatim</div>
+<div class="line"><a name="l00717"></a><span class="lineno"> 717</span> <span class="keywordtype">void</span> *<a class="code" href="utils_8h.html#ad7e1e137b3bf1f7108933d302a7f0177" title="Allocate space safely.">space</a> (<span class="keywordtype">unsigned</span> size)</div>
+<div class="line"><a name="l00718"></a><span class="lineno"> 718</span> \endverbatim</div>
+<div class="line"><a name="l00719"></a><span class="lineno"> 719</span> \copybrief <a class="code" href="utils_8h.html#ad7e1e137b3bf1f7108933d302a7f0177" title="Allocate space safely.">space</a>()</div>
+<div class="line"><a name="l00720"></a><span class="lineno"> 720</span> </div>
+<div class="line"><a name="l00721"></a><span class="lineno"> 721</span> \verbatim</div>
+<div class="line"><a name="l00722"></a><span class="lineno"> 722</span> <span class="keywordtype">void</span> *<a class="code" href="utils_8h.html#a9037ada838835b1b9db41581a021b0c8" title="Reallocate space safely.">xrealloc</a> ( <span class="keywordtype">void</span> *p,</div>
+<div class="line"><a name="l00723"></a><span class="lineno"> 723</span>  <span class="keywordtype">unsigned</span> size)</div>
+<div class="line"><a name="l00724"></a><span class="lineno"> 724</span> \endverbatim</div>
+<div class="line"><a name="l00725"></a><span class="lineno"> 725</span> \copybrief <a class="code" href="utils_8h.html#a9037ada838835b1b9db41581a021b0c8" title="Reallocate space safely.">xrealloc</a>()</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> \see utils.h <span class="keywordflow">for</span> a complete overview and detailed description of the utility functions</div>
+<div class="line"><a name="l00728"></a><span class="lineno"> 728</span> </div>
+<div class="line"><a name="l00729"></a><span class="lineno"> 729</span> \htmlonly</div>
+<div class="line"><a name="l00730"></a><span class="lineno"> 730</span> <hr></div>
+<div class="line"><a name="l00731"></a><span class="lineno"> 731</span> <a href=<span class="stringliteral">"#toc"</span>>Table of Contents</a></div>
+<div class="line"><a name="l00732"></a><span class="lineno"> 732</span> <hr></div>
+<div class="line"><a name="l00733"></a><span class="lineno"> 733</span> \endhtmlonly</div>
+<div class="line"><a name="l00734"></a><span class="lineno"> 734</span> </div>
+<div class="line"><a name="l00735"></a><span class="lineno"> 735</span> \ref mp_example <span class="stringliteral">"Next Page: Examples"</span></div>
+<div class="line"><a name="l00736"></a><span class="lineno"> 736</span> </div>
+<div class="line"><a name="l00737"></a><span class="lineno"> 737</span> \page mp_example Example - A Small Example Program</div>
+<div class="line"><a name="l00738"></a><span class="lineno"> 738</span> </div>
+<div class="line"><a name="l00739"></a><span class="lineno"> 739</span> The following program exercises most commonly used functions of the library.</div>
+<div class="line"><a name="l00740"></a><span class="lineno"> 740</span> The program folds two sequences <span class="keyword">using</span> both the mfe and partition <span class="keyword">function</span></div>
+<div class="line"><a name="l00741"></a><span class="lineno"> 741</span> algorithms and calculates the tree edit and profile distance of the</div>
+<div class="line"><a name="l00742"></a><span class="lineno"> 742</span> resulting structures and base pairing probabilities.</div>
+<div class="line"><a name="l00743"></a><span class="lineno"> 743</span> </div>
+<div class="line"><a name="l00744"></a><span class="lineno"> 744</span> \code{.c}</div>
+<div class="line"><a name="l00745"></a><span class="lineno"> 745</span> <span class="preprocessor">#include <stdio.h></span></div>
+<div class="line"><a name="l00746"></a><span class="lineno"> 746</span> <span class="preprocessor">#include <stdlib.h></span></div>
+<div class="line"><a name="l00747"></a><span class="lineno"> 747</span> <span class="preprocessor">#include <math.h></span></div>
+<div class="line"><a name="l00748"></a><span class="lineno"> 748</span> <span class="preprocessor">#include <string.h></span></div>
+<div class="line"><a name="l00749"></a><span class="lineno"> 749</span> <span class="preprocessor">#include "<a class="code" href="utils_8h.html" title="Various utility- and helper-functions used throughout the Vienna RNA package.">utils.h</a>"</span></div>
+<div class="line"><a name="l00750"></a><span class="lineno"> 750</span> <span class="preprocessor">#include "<a class="code" href="fold__vars_8h.html" title="Here all all declarations of the global variables used throughout RNAlib.">fold_vars.h</a>"</span></div>
+<div class="line"><a name="l00751"></a><span class="lineno"> 751</span> <span class="preprocessor">#include "<a class="code" href="fold_8h.html" title="MFE calculations and energy evaluations for single RNA sequences.">fold.h</a>"</span></div>
+<div class="line"><a name="l00752"></a><span class="lineno"> 752</span> <span class="preprocessor">#include "<a class="code" href="part__func_8h.html" title="Partition function of single RNA sequences.">part_func.h</a>"</span></div>
+<div class="line"><a name="l00753"></a><span class="lineno"> 753</span> <span class="preprocessor">#include "<a class="code" href="inverse_8h.html" title="Inverse folding routines.">inverse.h</a>"</span></div>
+<div class="line"><a name="l00754"></a><span class="lineno"> 754</span> <span class="preprocessor">#include "<a class="code" href="RNAstruct_8h.html" title="Parsing and Coarse Graining of Structures.">RNAstruct.h</a>"</span></div>
+<div class="line"><a name="l00755"></a><span class="lineno"> 755</span> <span class="preprocessor">#include "<a class="code" href="treedist_8h.html" title="Functions for Tree Edit Distances.">treedist.h</a>"</span></div>
+<div class="line"><a name="l00756"></a><span class="lineno"> 756</span> <span class="preprocessor">#include "<a class="code" href="stringdist_8h.html" title="Functions for String Alignment.">stringdist.h</a>"</span></div>
+<div class="line"><a name="l00757"></a><span class="lineno"> 757</span> <span class="preprocessor">#include "<a class="code" href="profiledist_8h.html">profiledist.h</a>"</span></div>
+<div class="line"><a name="l00758"></a><span class="lineno"> 758</span> </div>
+<div class="line"><a name="l00759"></a><span class="lineno"> 759</span> <span class="keywordtype">void</span> main()</div>
+<div class="line"><a name="l00760"></a><span class="lineno"> 760</span> {</div>
+<div class="line"><a name="l00761"></a><span class="lineno"> 761</span>  <span class="keywordtype">char</span> *seq1=<span class="stringliteral">"CGCAGGGAUACCCGCG"</span>, *seq2=<span class="stringliteral">"GCGCCCAUAGGGACGC"</span>,</div>
+<div class="line"><a name="l00762"></a><span class="lineno"> 762</span>  *struct1,* struct2,* xstruc;</div>
+<div class="line"><a name="l00763"></a><span class="lineno"> 763</span>  <span class="keywordtype">float</span> e1, e2, tree_dist, string_dist, profile_dist, kT;</div>
+<div class="line"><a name="l00764"></a><span class="lineno"> 764</span>  <a class="code" href="structTree.html">Tree</a> *T1, *T2;</div>
+<div class="line"><a name="l00765"></a><span class="lineno"> 765</span>  <a class="code" href="structswString.html">swString</a> *S1, *S2;</div>
+<div class="line"><a name="l00766"></a><span class="lineno"> 766</span>  <span class="keywordtype">float</span> *pf1, *pf2;</div>
+<div class="line"><a name="l00767"></a><span class="lineno"> 767</span>  FLT_OR_DBL *bppm;</div>
+<div class="line"><a name="l00768"></a><span class="lineno"> 768</span>  <span class="comment">/* fold at 30C instead of the default 37C */</span></div>
+<div class="line"><a name="l00769"></a><span class="lineno"> 769</span>  <a class="code" href="fold__vars_8h.html#ab4b11c8d9c758430960896bc3fe82ead" title="Rescale energy parameters to a temperature in degC.">temperature</a> = 30.; <span class="comment">/* must be set *before* initializing */</span></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="comment">/* allocate memory for structure and fold */</span></div>
+<div class="line"><a name="l00772"></a><span class="lineno"> 772</span>  struct1 = (<span class="keywordtype">char</span>* ) <a class="code" href="utils_8h.html#ad7e1e137b3bf1f7108933d302a7f0177" title="Allocate space safely.">space</a>(<span class="keyword">sizeof</span>(<span class="keywordtype">char</span>)*(strlen(seq1)+1));</div>
+<div class="line"><a name="l00773"></a><span class="lineno"> 773</span>  e1 = <a class="code" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b" title="Compute minimum free energy and an appropriate secondary structure of an RNA sequence.">fold</a>(seq1, struct1);</div>
+<div class="line"><a name="l00774"></a><span class="lineno"> 774</span> </div>
+<div class="line"><a name="l00775"></a><span class="lineno"> 775</span>  struct2 = (<span class="keywordtype">char</span>* ) <a class="code" href="utils_8h.html#ad7e1e137b3bf1f7108933d302a7f0177" title="Allocate space safely.">space</a>(<span class="keyword">sizeof</span>(<span class="keywordtype">char</span>)*(strlen(seq2)+1));</div>
+<div class="line"><a name="l00776"></a><span class="lineno"> 776</span>  e2 = <a class="code" href="group__mfe__fold.html#gaadafcb0f140795ae62e5ca027e335a9b" title="Compute minimum free energy and an appropriate secondary structure of an RNA sequence.">fold</a>(seq2, struct2);</div>
+<div class="line"><a name="l00777"></a><span class="lineno"> 777</span> </div>
+<div class="line"><a name="l00778"></a><span class="lineno"> 778</span>  <a class="code" href="group__mfe__fold.html#ga107fdfe5fd641868156bfd849f6866c7" title="Free arrays for mfe folding.">free_arrays</a>(); <span class="comment">/* free arrays used in fold() */</span></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="comment">/* produce tree and string representations for comparison */</span></div>
+<div class="line"><a name="l00781"></a><span class="lineno"> 781</span>  xstruc = <a class="code" href="RNAstruct_8h.html#a78d73cd54a068ef2812812771cdddc6f" title="Convert the full structure from bracket notation to the expanded notation including root...">expand_Full</a>(struct1);</div>
+<div class="line"><a name="l00782"></a><span class="lineno"> 782</span>  T1 = <a class="code" href="treedist_8h.html#a08fe4d5afd385dce593b86eaf010c6e3" title="Constructs a Tree ( essentially the postorder list ) of the structure 'struc', for use in tree_edit_d...">make_tree</a>(xstruc);</div>
+<div class="line"><a name="l00783"></a><span class="lineno"> 783</span>  S1 = <a class="code" href="stringdist_8h.html#a3125991b3a403b3f89230474deb3f22e" title="Convert a structure into a format suitable for string_edit_distance().">Make_swString</a>(xstruc);</div>
+<div class="line"><a name="l00784"></a><span class="lineno"> 784</span>  free(xstruc);</div>
+<div class="line"><a name="l00785"></a><span class="lineno"> 785</span> </div>
+<div class="line"><a name="l00786"></a><span class="lineno"> 786</span>  xstruc = <a class="code" href="RNAstruct_8h.html#a78d73cd54a068ef2812812771cdddc6f" title="Convert the full structure from bracket notation to the expanded notation including root...">expand_Full</a>(struct2);</div>
+<div class="line"><a name="l00787"></a><span class="lineno"> 787</span>  T2 = <a class="code" href="treedist_8h.html#a08fe4d5afd385dce593b86eaf010c6e3" title="Constructs a Tree ( essentially the postorder list ) of the structure 'struc', for use in tree_edit_d...">make_tree</a>(xstruc);</div>
+<div class="line"><a name="l00788"></a><span class="lineno"> 788</span>  S2 = <a class="code" href="stringdist_8h.html#a3125991b3a403b3f89230474deb3f22e" title="Convert a structure into a format suitable for string_edit_distance().">Make_swString</a>(xstruc);</div>
+<div class="line"><a name="l00789"></a><span class="lineno"> 789</span>  free(xstruc);</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="comment">/* calculate tree edit distance and aligned structures with gaps */</span></div>
+<div class="line"><a name="l00792"></a><span class="lineno"> 792</span>  <a class="code" href="dist__vars_8h.html#aa03194c513af6b860e7b33e370b82bdb" title="Produce an alignment of the two structures being compared by tracing the editing path giving the mini...">edit_backtrack</a> = 1;</div>
+<div class="line"><a name="l00793"></a><span class="lineno"> 793</span>  tree_dist = <a class="code" href="treedist_8h.html#a3b21f1925f7071f46d93431a835217bb" title="Calculates the edit distance of the two trees.">tree_edit_distance</a>(T1, T2);</div>
+<div class="line"><a name="l00794"></a><span class="lineno"> 794</span>  <a class="code" href="treedist_8h.html#acbc1cb9bce582ea945e4a467c76a57aa" title="Free the memory allocated for Tree t.">free_tree</a>(T1); <a class="code" href="treedist_8h.html#acbc1cb9bce582ea945e4a467c76a57aa" title="Free the memory allocated for Tree t.">free_tree</a>(T2);</div>
+<div class="line"><a name="l00795"></a><span class="lineno"> 795</span>  <a class="code" href="RNAstruct_8h.html#a1054c4477d53b31d79d4cb132100e87a" title="Converts two aligned structures in expanded notation.">unexpand_aligned_F</a>(aligned_line);</div>
+<div class="line"><a name="l00796"></a><span class="lineno"> 796</span>  printf(<span class="stringliteral">"%s\n%s %3.2f\n"</span>, aligned_line[0], aligned_line[1], tree_dist);</div>
+<div class="line"><a name="l00797"></a><span class="lineno"> 797</span> </div>
+<div class="line"><a name="l00798"></a><span class="lineno"> 798</span>  <span class="comment">/* same thing using string edit (alignment) distance */</span></div>
+<div class="line"><a name="l00799"></a><span class="lineno"> 799</span>  string_dist = <a class="code" href="stringdist_8h.html#a89e3c335ef17780576d7c0e713830db9" title="Calculate the string edit distance of T1 and T2.">string_edit_distance</a>(S1, S2);</div>
+<div class="line"><a name="l00800"></a><span class="lineno"> 800</span>  free(S1); free(S2);</div>
+<div class="line"><a name="l00801"></a><span class="lineno"> 801</span>  printf(<span class="stringliteral">"%s mfe=%5.2f\n%s mfe=%5.2f dist=%3.2f\n"</span>,</div>
+<div class="line"><a name="l00802"></a><span class="lineno"> 802</span>  aligned_line[0], e1, aligned_line[1], e2, string_dist);</div>
+<div class="line"><a name="l00803"></a><span class="lineno"> 803</span> </div>
+<div class="line"><a name="l00804"></a><span class="lineno"> 804</span>  <span class="comment">/* for longer sequences one should also set a scaling factor for</span></div>
+<div class="line"><a name="l00805"></a><span class="lineno"> 805</span> <span class="comment"> partition function folding, e.g: */</span></div>
+<div class="line"><a name="l00806"></a><span class="lineno"> 806</span>  kT = (<a class="code" href="fold__vars_8h.html#ab4b11c8d9c758430960896bc3fe82ead" title="Rescale energy parameters to a temperature in degC.">temperature</a>+273.15)*1.98717/1000.; <span class="comment">/* kT in kcal/mol */</span></div>
+<div class="line"><a name="l00807"></a><span class="lineno"> 807</span>  <a class="code" href="fold__vars_8h.html#ad3b22044065acc6dee0af68931b52cfd" title="A scaling factor used by pf_fold() to avoid overflows.">pf_scale</a> = exp(-e1/kT/strlen(seq1));</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>  <span class="comment">/* calculate partition function and base pair probabilities */</span></div>
+<div class="line"><a name="l00810"></a><span class="lineno"> 810</span>  e1 = <a class="code" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold</a>(seq1, struct1);</div>
+<div class="line"><a name="l00811"></a><span class="lineno"> 811</span>  <span class="comment">/* get the base pair probability matrix for the previous run of pf_fold() */</span></div>
+<div class="line"><a name="l00812"></a><span class="lineno"> 812</span>  bppm = <a class="code" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115" title="Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i...">export_bppm</a>();</div>
+<div class="line"><a name="l00813"></a><span class="lineno"> 813</span>  pf1 = <a class="code" href="profiledist_8h.html#a8822fd5268be115c6e6cdc92009436cc" title="condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired.">Make_bp_profile_bppm</a>(bppm, strlen(seq1));</div>
+<div class="line"><a name="l00814"></a><span class="lineno"> 814</span> </div>
+<div class="line"><a name="l00815"></a><span class="lineno"> 815</span>  e2 = <a class="code" href="group__pf__fold.html#gadc3db3d98742427e7001a7fd36ef28c2" title="Compute the partition function of an RNA sequence.">pf_fold</a>(seq2, struct2);</div>
+<div class="line"><a name="l00816"></a><span class="lineno"> 816</span>  <span class="comment">/* get the base pair probability matrix for the previous run of pf_fold() */</span></div>
+<div class="line"><a name="l00817"></a><span class="lineno"> 817</span>  bppm = <a class="code" href="group__pf__fold.html#ga6d463707d5f64bdc4d21515b7dd9b115" title="Get a pointer to the base pair probability arrayAccessing the base pair probabilities for a pair (i...">export_bppm</a>();</div>
+<div class="line"><a name="l00818"></a><span class="lineno"> 818</span>  pf2 = <a class="code" href="profiledist_8h.html#a8822fd5268be115c6e6cdc92009436cc" title="condense pair probability matrix into a vector containing probabilities for unpaired, upstream paired and downstream paired.">Make_bp_profile_bppm</a>(bppm, strlen(seq2));</div>
+<div class="line"><a name="l00819"></a><span class="lineno"> 819</span> </div>
+<div class="line"><a name="l00820"></a><span class="lineno"> 820</span>  <a class="code" href="group__pf__fold.html#gae73db3f49a94f0f72e067ecd12681dbd" title="Free arrays for the partition function recursions.">free_pf_arrays</a>(); <span class="comment">/* free space allocated for pf_fold() */</span></div>
+<div class="line"><a name="l00821"></a><span class="lineno"> 821</span> </div>
+<div class="line"><a name="l00822"></a><span class="lineno"> 822</span>  profile_dist = <a class="code" href="profiledist_8h.html#abe75e90e00a1e5dd8862944ed53dad5d" title="Align the 2 probability profiles T1, T2 .">profile_edit_distance</a>(pf1, pf2);</div>
+<div class="line"><a name="l00823"></a><span class="lineno"> 823</span>  printf(<span class="stringliteral">"%s free energy=%5.2f\n%s free energy=%5.2f dist=%3.2f\n"</span>,</div>
+<div class="line"><a name="l00824"></a><span class="lineno"> 824</span>  aligned_line[0], e1, aligned_line[1], e2, profile_dist);</div>
+<div class="line"><a name="l00825"></a><span class="lineno"> 825</span> </div>
+<div class="line"><a name="l00826"></a><span class="lineno"> 826</span>  <a class="code" href="profiledist_8h.html#a9b0b84a5a45761bf42d7c835dcdb3b85" title="free space allocated in Make_bp_profile">free_profile</a>(pf1); <a class="code" href="profiledist_8h.html#a9b0b84a5a45761bf42d7c835dcdb3b85" title="free space allocated in Make_bp_profile">free_profile</a>(pf2);</div>
+<div class="line"><a name="l00827"></a><span class="lineno"> 827</span> }</div>
+<div class="line"><a name="l00828"></a><span class="lineno"> 828</span> \endcode</div>
+<div class="line"><a name="l00829"></a><span class="lineno"> 829</span> </div>
+<div class="line"><a name="l00830"></a><span class="lineno"> 830</span> In a typical Unix environment you would compile <span class="keyword">this</span> program <span class="keyword">using</span>:</div>
+<div class="line"><a name="l00831"></a><span class="lineno"> 831</span> \verbatim</div>
+<div class="line"><a name="l00832"></a><span class="lineno"> 832</span> cc ${OPENMP_CFLAGS} -c example.c -I${hpath}</div>
+<div class="line"><a name="l00833"></a><span class="lineno"> 833</span> \endverbatim</div>
+<div class="line"><a name="l00834"></a><span class="lineno"> 834</span> and link using</div>
+<div class="line"><a name="l00835"></a><span class="lineno"> 835</span> \verbatim</div>
+<div class="line"><a name="l00836"></a><span class="lineno"> 836</span> cc ${OPENMP_CFLAGS} -o example -L${lpath} -lRNA -lm</div>
+<div class="line"><a name="l00837"></a><span class="lineno"> 837</span> \endverbatim</div>
+<div class="line"><a name="l00838"></a><span class="lineno"> 838</span> where \e ${hpath} and \e ${lpath} point to the location of the header</div>
+<div class="line"><a name="l00839"></a><span class="lineno"> 839</span> files and library, respectively.</div>
+<div class="line"><a name="l00840"></a><span class="lineno"> 840</span> \note As <span class="keywordflow">default</span>, the RNAlib is compiled with build-in \e OpenMP multithreading</div>
+<div class="line"><a name="l00841"></a><span class="lineno"> 841</span> support. Thus, when linking your own <span class="keywordtype">object</span> files to the library you have to pass</div>
+<div class="line"><a name="l00842"></a><span class="lineno"> 842</span> the compiler specific \e ${OPENMP_CFLAGS} (e.g. <span class="stringliteral">'-fopenmp'</span> for \b gcc) even <span class="keywordflow">if</span> your code does not</div>
+<div class="line"><a name="l00843"></a><span class="lineno"> 843</span> use openmp specific code. However, in that <span class="keywordflow">case</span> the \e OpenMP flags may be ommited when compiling</div>
+<div class="line"><a name="l00844"></a><span class="lineno"> 844</span> example.c</div>
+<div class="line"><a name="l00845"></a><span class="lineno"> 845</span> </div>
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