-\label{mp_utils_toc}%
-\hypertarget{mp_utils_toc}{}%
- \subsubsection*{Table of Contents}
+\label{mp_utils_toc}
+\hypertarget{mp_utils_toc}{}
+
+
+\subsubsection*{Table of Contents}
\begin{DoxyItemize}
-\item \hyperlink{mp_utils_utils_ss}{Producing secondary structure graphs} \item \hyperlink{mp_utils_utils_dot}{Producing (colored) dot plots for base pair probabilities} \item \hyperlink{mp_utils_utils_aln}{Producing (colored) alignments} \item \hyperlink{mp_utils_utils_seq}{R\-N\-A sequence related utilities} \item \hyperlink{mp_utils_utils_struc}{R\-N\-A secondary structure related utilities} \item \hyperlink{mp_utils_utils_misc}{Miscellaneous Utilities}\end{DoxyItemize}
+\item \hyperlink{mp_utils_utils_ss}{Producing secondary structure graphs} \item \hyperlink{mp_utils_utils_dot}{Producing (colored) dot plots for base pair probabilities} \item \hyperlink{mp_utils_utils_aln}{Producing (colored) alignments} \item \hyperlink{mp_utils_utils_seq}{RNA sequence related utilities} \item \hyperlink{mp_utils_utils_struc}{RNA secondary structure related utilities} \item \hyperlink{mp_utils_utils_misc}{Miscellaneous Utilities}\end{DoxyItemize}
\hypertarget{mp_utils_utils_ss}{}\section{Producing secondary structure graphs}\label{mp_utils_utils_ss}
-\begin{DoxyVerb}int PS_rna_plot ( char *string,
+\begin{DoxyVerb}
+int PS_rna_plot ( char *string,
char *structure,
char *file)
\end{DoxyVerb}
- Produce a secondary structure graph in Post\-Script and write it to 'filename'.
\ No newline at end of file
+ Produce a secondary structure graph in PostScript and write it to 'filename'.
+
+\begin{DoxyVerb}
+int PS_rna_plot_a (
+ char *string,
+ char *structure,
+ char *file,
+ char *pre,
+ char *post)
+\end{DoxyVerb}
+ Produce a secondary structure graph in PostScript including additional annotation macros and write it to 'filename'.
+
+\begin{DoxyVerb}
+int gmlRNA (char *string,
+ char *structure,
+ char *ssfile,
+ char option)
+\end{DoxyVerb}
+ Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file.
+
+\begin{DoxyVerb}
+int ssv_rna_plot (char *string,
+ char *structure,
+ char *ssfile)
+\end{DoxyVerb}
+ Produce a secondary structure graph in SStructView format.
+
+\begin{DoxyVerb}
+int svg_rna_plot (char *string,
+ char *structure,
+ char *ssfile)
+\end{DoxyVerb}
+ Produce a secondary structure plot in SVG format and write it to a file.
+
+\begin{DoxyVerb}
+int xrna_plot ( char *string,
+ char *structure,
+ char *ssfile)
+\end{DoxyVerb}
+ Produce a secondary structure plot for further editing in XRNA.
+
+\begin{DoxyVerb}
+int rna_plot_type
+\end{DoxyVerb}
+ Switch for changing the secondary structure layout algorithm.
+
+Two low-\/level functions provide direct access to the graph lauyouting algorithms:
+
+\begin{DoxyVerb}
+int simple_xy_coordinates ( short *pair_table,
+ float *X,
+ float *Y)
+\end{DoxyVerb}
+ Calculate nucleotide coordinates for secondary structure plot the {\itshape Simple way\/}.
+
+\begin{DoxyVerb}
+int naview_xy_coordinates ( short *pair_table,
+ float *X,
+ float *Y)
+\end{DoxyVerb}
+
+
+\begin{DoxySeeAlso}{See also}
+\hyperlink{PS__dot_8h}{PS\_\-dot.h} and \hyperlink{naview_8h}{naview.h} for more detailed descriptions.
+\end{DoxySeeAlso}
+\hypertarget{mp_utils_utils_dot}{}\section{Producing (colored) dot plots for base pair probabilities}\label{mp_utils_utils_dot}
+\begin{DoxyVerb}
+int PS_color_dot_plot ( char *string,
+ cpair *pi,
+ char *filename)
+\end{DoxyVerb}
+
+
+\begin{DoxyVerb}
+int PS_color_dot_plot_turn (char *seq,
+ cpair *pi,
+ char *filename,
+ int winSize)
+\end{DoxyVerb}
+
+
+\begin{DoxyVerb}
+int PS_dot_plot_list (char *seq,
+ char *filename,
+ plist *pl,
+ plist *mf,
+ char *comment)
+\end{DoxyVerb}
+ Produce a postscript dot-\/plot from two pair lists.
+
+\begin{DoxyVerb}
+int PS_dot_plot_turn (char *seq,
+ struct plist *pl,
+ char *filename,
+ int winSize)
+\end{DoxyVerb}
+
+
+\begin{DoxySeeAlso}{See also}
+\hyperlink{PS__dot_8h}{PS\_\-dot.h} for more detailed descriptions.
+\end{DoxySeeAlso}
+\hypertarget{mp_utils_utils_aln}{}\section{Producing (colored) alignments}\label{mp_utils_utils_aln}
+\begin{DoxyVerb}
+int PS_color_aln (
+ const char *structure,
+ const char *filename,
+ const char *seqs[],
+ const char *names[])
+\end{DoxyVerb}
+
+
+\hypertarget{mp_utils_utils_seq}{}\section{RNA sequence related utilities}\label{mp_utils_utils_seq}
+Several functions provide useful applications to RNA sequences
+
+\begin{DoxyVerb}
+char *random_string (int l,
+ const char symbols[])
+\end{DoxyVerb}
+ Create a random string using characters from a specified symbol set.
+
+\begin{DoxyVerb}
+int hamming ( const char *s1,
+ const char *s2)
+\end{DoxyVerb}
+ Calculate hamming distance between two sequences.
+
+\begin{DoxyVerb}
+void str_DNA2RNA(char *sequence);
+\end{DoxyVerb}
+ Convert a DNA input sequence to RNA alphabet.
+
+\begin{DoxyVerb}
+void str_uppercase(char *sequence);
+\end{DoxyVerb}
+ Convert an input sequence to uppercase.
+
+\hypertarget{mp_utils_utils_struc}{}\section{RNA secondary structure related utilities}\label{mp_utils_utils_struc}
+\begin{DoxyVerb}
+char *pack_structure (const char *struc)
+\end{DoxyVerb}
+ Pack secondary secondary structure, 5:1 compression using base 3 encoding.
+
+\begin{DoxyVerb}
+char *unpack_structure (const char *packed)
+\end{DoxyVerb}
+ Unpack secondary structure previously packed with \hyperlink{utils_8h_ac6dfa5e22928c087c6e09ff0054a7ced}{pack\_\-structure()}.
+
+\begin{DoxyVerb}
+short *make_pair_table (const char *structure)
+\end{DoxyVerb}
+ Create a pair table of a secondary structure.
+
+\begin{DoxyVerb}
+short *copy_pair_table (const short *pt)
+\end{DoxyVerb}
+ Get an exact copy of a pair table.
+
+\hypertarget{mp_utils_utils_misc}{}\section{Miscellaneous Utilities}\label{mp_utils_utils_misc}
+\begin{DoxyVerb}
+void print_tty_input_seq (void)
+\end{DoxyVerb}
+ Print a line to {\itshape stdout\/} that asks for an input sequence.
+
+\begin{DoxyVerb}
+void print_tty_constraint_full (void)
+\end{DoxyVerb}
+ Print structure constraint characters to stdout (full constraint support).
+
+\begin{DoxyVerb}
+void print_tty_constraint (unsigned int option)
+\end{DoxyVerb}
+ Print structure constraint characters to stdout. (constraint support is specified by option parameter).
+
+\begin{DoxyVerb}
+int *get_iindx (unsigned int length)
+\end{DoxyVerb}
+ Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions.
+
+\begin{DoxyVerb}
+int *get_indx (unsigned int length)
+\end{DoxyVerb}
+ Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions.
+
+\begin{DoxyVerb}
+void constrain_ptypes (
+ const char *constraint,
+ unsigned int length,
+ char *ptype,
+ int *BP,
+ int min_loop_size,
+ unsigned int idx_type)
+\end{DoxyVerb}
+ Insert constraining pair types according to constraint structure string.
+
+\begin{DoxyVerb}
+char *get_line(FILE *fp);
+\end{DoxyVerb}
+ Read a line of arbitrary length from a stream.
+
+\begin{DoxyVerb}
+unsigned int read_record(
+ char **header,
+ char **sequence,
+ char ***rest,
+ unsigned int options);
+\end{DoxyVerb}
+ Get a data record from stdin.
+
+\begin{DoxyVerb}
+char *time_stamp (void)
+\end{DoxyVerb}
+ Get a timestamp.
+
+\begin{DoxyVerb}
+void warn_user (const char message[])
+\end{DoxyVerb}
+ Print a warning message.
+
+\begin{DoxyVerb}
+void nrerror (const char message[])
+\end{DoxyVerb}
+ Die with an error message.
+
+\begin{DoxyVerb}
+void init_rand (void)
+\end{DoxyVerb}
+ Make random number seeds.
+
+\begin{DoxyVerb}
+unsigned short xsubi[3];
+\end{DoxyVerb}
+ Current 48 bit random number.
+
+\begin{DoxyVerb}
+double urn (void)
+\end{DoxyVerb}
+ get a random number from \mbox{[}0..1\mbox{]}
+
+\begin{DoxyVerb}
+int int_urn (int from, int to)
+\end{DoxyVerb}
+ Generates a pseudo random integer in a specified range.
+
+\begin{DoxyVerb}
+void *space (unsigned size)
+\end{DoxyVerb}
+ Allocate space safely.
+
+\begin{DoxyVerb}
+void *xrealloc ( void *p,
+ unsigned size)
+\end{DoxyVerb}
+ Reallocate space safely.
+
+\begin{DoxySeeAlso}{See also}
+\hyperlink{utils_8h}{utils.h} for a complete overview and detailed description of the utility functions
+\end{DoxySeeAlso}
+
+
+\hyperlink{mp_example}{Next Page: Examples}
\ No newline at end of file
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