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+<div class="title">Utilities - Odds and Ends </div> </div>
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+<div class="contents">
+<div class="textblock"><p><a class="anchor" id="toc"></a> </p>
+<h3>Table of Contents</h3>
+<hr/>
+<ul>
+<li><a class="el" href="mp_utils.html#utils_ss">Producing secondary structure graphs</a> </li>
+<li><a class="el" href="mp_utils.html#utils_dot">Producing (colored) dot plots for base pair probabilities</a> </li>
+<li><a class="el" href="mp_utils.html#utils_aln">Producing (colored) alignments</a> </li>
+<li><a class="el" href="mp_utils.html#utils_seq">RNA sequence related utilities</a> </li>
+<li><a class="el" href="mp_utils.html#utils_struc">RNA secondary structure related utilities</a> </li>
+<li><a class="el" href="mp_utils.html#utils_misc">Miscellaneous Utilities</a></li>
+</ul>
+<hr/>
+<h1><a class="anchor" id="utils_ss"></a>
+Producing secondary structure graphs</h1>
+<pre class="fragment">int PS_rna_plot ( char *string,
+ char *structure,
+ char *file)
+</pre><p> Produce a secondary structure graph in PostScript and write it to 'filename'. </p>
+<pre class="fragment">int PS_rna_plot_a (
+ char *string,
+ char *structure,
+ char *file,
+ char *pre,
+ char *post)
+</pre><p> Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'. </p>
+<pre class="fragment">int gmlRNA (char *string,
+ char *structure,
+ char *ssfile,
+ char option)
+</pre><p> Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file. </p>
+<pre class="fragment">int ssv_rna_plot (char *string,
+ char *structure,
+ char *ssfile)
+</pre><p> Produce a secondary structure graph in SStructView format. </p>
+<pre class="fragment">int svg_rna_plot (char *string,
+ char *structure,
+ char *ssfile)
+</pre><p> Produce a secondary structure plot in SVG format and write it to a file. </p>
+<pre class="fragment">int xrna_plot ( char *string,
+ char *structure,
+ char *ssfile)
+</pre><p> Produce a secondary structure plot for further editing in XRNA. </p>
+<pre class="fragment">int rna_plot_type
+</pre><p> Switch for changing the secondary structure layout algorithm. </p>
+<p>Two low-level functions provide direct access to the graph lauyouting algorithms:</p>
+<pre class="fragment">int simple_xy_coordinates ( short *pair_table,
+ float *X,
+ float *Y)
+</pre><p> Calculate nucleotide coordinates for secondary structure plot the <em>Simple way</em> </p>
+<pre class="fragment">int naview_xy_coordinates ( short *pair_table,
+ float *X,
+ float *Y)
+</pre> <dl class="section see"><dt>See also:</dt><dd><a class="el" href="PS__dot_8h.html" title="Various functions for plotting RNA secondary structures, dot-plots and other visualizations.">PS_dot.h</a> and <a class="el" href="naview_8h.html">naview.h</a> for more detailed descriptions.</dd></dl>
+
+<hr>
+<a href="#toc">Table of Contents</a>
+<hr>
+<h1><a class="anchor" id="utils_dot"></a>
+Producing (colored) dot plots for base pair probabilities</h1>
+<pre class="fragment">int PS_color_dot_plot ( char *string,
+ cpair *pi,
+ char *filename)
+</pre> <pre class="fragment">int PS_color_dot_plot_turn (char *seq,
+ cpair *pi,
+ char *filename,
+ int winSize)
+</pre> <pre class="fragment">int PS_dot_plot_list (char *seq,
+ char *filename,
+ plist *pl,
+ plist *mf,
+ char *comment)
+</pre><p> Produce a postscript dot-plot from two pair lists. </p>
+<pre class="fragment">int PS_dot_plot_turn (char *seq,
+ struct plist *pl,
+ char *filename,
+ int winSize)
+</pre> <dl class="section see"><dt>See also:</dt><dd><a class="el" href="PS__dot_8h.html" title="Various functions for plotting RNA secondary structures, dot-plots and other visualizations.">PS_dot.h</a> for more detailed descriptions.</dd></dl>
+<h1><a class="anchor" id="utils_aln"></a>
+Producing (colored) alignments</h1>
+<pre class="fragment">int PS_color_aln (
+ const char *structure,
+ const char *filename,
+ const char *seqs[],
+ const char *names[])
+</pre>
+<hr>
+<a href="#toc">Table of Contents</a>
+<hr>
+<h1><a class="anchor" id="utils_seq"></a>
+RNA sequence related utilities</h1>
+<p>Several functions provide useful applications to RNA sequences</p>
+<pre class="fragment">char *random_string (int l,
+ const char symbols[])
+</pre><p> Create a random string using characters from a specified symbol set. </p>
+<pre class="fragment">int hamming ( const char *s1,
+ const char *s2)
+</pre><p> Calculate hamming distance between two sequences. </p>
+<pre class="fragment">void str_DNA2RNA(char *sequence);
+</pre><p> Convert a DNA input sequence to RNA alphabet. </p>
+<pre class="fragment">void str_uppercase(char *sequence);
+</pre><p> Convert an input sequence to uppercase. </p>
+
+<hr>
+<a href="#toc">Table of Contents</a>
+<hr>
+<h1><a class="anchor" id="utils_struc"></a>
+RNA secondary structure related utilities</h1>
+<pre class="fragment">char *pack_structure (const char *struc)
+</pre><p> Pack secondary secondary structure, 5:1 compression using base 3 encoding. </p>
+<pre class="fragment">char *unpack_structure (const char *packed)
+</pre><p> Unpack secondary structure previously packed with <a class="el" href="utils_8h.html#ac6dfa5e22928c087c6e09ff0054a7ced" title="Pack secondary secondary structure, 5:1 compression using base 3 encoding.">pack_structure()</a> </p>
+<pre class="fragment">short *make_pair_table (const char *structure)
+</pre><p> Create a pair table of a secondary structure. </p>
+<pre class="fragment">short *copy_pair_table (const short *pt)
+</pre><p> Get an exact copy of a pair table. </p>
+
+<hr>
+<a href="#toc">Table of Contents</a>
+<hr>
+<h1><a class="anchor" id="utils_misc"></a>
+Miscellaneous Utilities</h1>
+<pre class="fragment">void print_tty_input_seq (void)
+</pre><p> Print a line to <em>stdout</em> that asks for an input sequence. </p>
+<pre class="fragment">void print_tty_constraint_full (void)
+</pre><p> Print structure constraint characters to stdout (full constraint support) </p>
+<pre class="fragment">void print_tty_constraint (unsigned int option)
+</pre><p> Print structure constraint characters to stdout. (constraint support is specified by option parameter) </p>
+<pre class="fragment">int *get_iindx (unsigned int length)
+</pre><p> Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions. </p>
+<pre class="fragment">int *get_indx (unsigned int length)
+</pre><p> Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions. </p>
+<pre class="fragment">void constrain_ptypes (
+ const char *constraint,
+ unsigned int length,
+ char *ptype,
+ int *BP,
+ int min_loop_size,
+ unsigned int idx_type)
+</pre><p> Insert constraining pair types according to constraint structure string. </p>
+<pre class="fragment">char *get_line(FILE *fp);
+</pre><p> Read a line of arbitrary length from a stream. </p>
+<pre class="fragment">unsigned int read_record(
+ char **header,
+ char **sequence,
+ char ***rest,
+ unsigned int options);
+</pre><p> Get a data record from stdin. </p>
+<pre class="fragment">char *time_stamp (void)
+</pre><p> Get a timestamp. </p>
+<pre class="fragment">void warn_user (const char message[])
+</pre><p> Print a warning message. </p>
+<pre class="fragment">void nrerror (const char message[])
+</pre><p> Die with an error message. </p>
+<pre class="fragment">void init_rand (void)
+</pre><p> Make random number seeds. </p>
+<pre class="fragment">unsigned short xsubi[3];
+</pre><p> Current 48 bit random number. </p>
+<pre class="fragment">double urn (void)
+</pre><p> get a random number from [0..1] </p>
+<pre class="fragment">int int_urn (int from, int to)
+</pre><p> Generates a pseudo random integer in a specified range. </p>
+<pre class="fragment">void *space (unsigned size)
+</pre><p> Allocate space safely. </p>
+<pre class="fragment">void *xrealloc ( void *p,
+ unsigned size)
+</pre><p> Reallocate space safely. </p>
+<dl class="section see"><dt>See also:</dt><dd><a class="el" href="utils_8h.html" title="Various utility- and helper-functions used throughout the Vienna RNA package.">utils.h</a> for a complete overview and detailed description of the utility functions</dd></dl>
+
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+<hr>
+<p><a class="el" href="mp_example.html">Next Page: Examples</a> </p>
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