binaries/src/ViennaRNA/doc/latex/pair__mat_8h_source.tex

   1 \hypertarget{pair__mat_8h}{\section{pair\-\_\-mat.\-h}
   2 \label{pair__mat_8h}\index{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/pair\-\_\-mat.\-h@{/home/asherstnev/\-Projects/\-Java.\-projects/jabaws/secure-\/git/develop/binaries/src/\-Vienna\-R\-N\-A/\-H/pair\-\_\-mat.\-h}}
   3 }
   4
   5 \begin{DoxyCode}
   6 00001 \textcolor{preprocessor}{#include <ctype.h>}
   7 00002 \textcolor{preprocessor}{#include "\hyperlink{utils_8h}{utils.h}"}
   8 00003 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold\_vars.h}"}
   9 00004
  10 00005 \textcolor{preprocessor}{#define NBASES 8}
  11 00006 \textcolor{preprocessor}{}\textcolor{comment}{/*@notnull@*/}
  12 00007
  13 00008 \textcolor{keyword}{static} \textcolor{keyword}{const} \textcolor{keywordtype}{char} Law\_and\_Order[] = \textcolor{stringliteral}{"\_ACGUTXKI"};
  14 00009 \textcolor{keyword}{static} \textcolor{keywordtype}{int} BP\_pair[NBASES][NBASES]=
  15 00010 \textcolor{comment}{/* \_  A  C  G  U  X  K  I */}
  16 00011 \{\{ 0, 0, 0, 0, 0, 0, 0, 0\},
  17 00012  \{ 0, 0, 0, 0, 5, 0, 0, 5\},
  18 00013  \{ 0, 0, 0, 1, 0, 0, 0, 0\},
  19 00014  \{ 0, 0, 2, 0, 3, 0, 0, 0\},
  20 00015  \{ 0, 6, 0, 4, 0, 0, 0, 6\},
  21 00016  \{ 0, 0, 0, 0, 0, 0, 2, 0\},
  22 00017  \{ 0, 0, 0, 0, 0, 1, 0, 0\},
  23 00018  \{ 0, 6, 0, 0, 5, 0, 0, 0\}\};
  24 00019
  25 00020 \textcolor{preprocessor}{#define MAXALPHA 20       }\textcolor{comment}{/* maximal length of alphabet */}\textcolor{preprocessor}{}
  26 00021 \textcolor{preprocessor}{}
  27 00022 \textcolor{keyword}{static} \textcolor{keywordtype}{short} alias[\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1];
  28 00023 \textcolor{keyword}{static} \textcolor{keywordtype}{int} pair[\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1][\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1];
  29 00024 \textcolor{comment}{/* rtype[pair[i][j]]:=pair[j][i] */}
  30 00025 \textcolor{keyword}{static} \textcolor{keywordtype}{int} rtype[8] = \{0, 2, 1, 4, 3, 6, 5, 7\};
  31 00026
  32 00027 \textcolor{preprocessor}{#ifdef \_OPENMP}
  33 00028 \textcolor{preprocessor}{}\textcolor{preprocessor}{#pragma omp threadprivate(Law\_and\_Order, BP\_pair, alias, pair, rtype)}
  34 00029 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
  35 00030 \textcolor{preprocessor}{}
  36 00031 \textcolor{comment}{/* for backward compatibility */}
  37 00032 \textcolor{preprocessor}{#define ENCODE(c) encode\_char(c)}
  38 00033 \textcolor{preprocessor}{}
  39 00034 \textcolor{keyword}{static} \textcolor{keywordtype}{int} encode\_char(\textcolor{keywordtype}{char} c) \{
  40 00035   \textcolor{comment}{/* return numerical representation of base used e.g. in pair[][] */}
  41 00036   \textcolor{keywordtype}{int} code;
  42 00037   \textcolor{keywordflow}{if} (energy\_set>0) code = (int) (c-\textcolor{charliteral}{'A'})+1;
  43 00038   \textcolor{keywordflow}{else} \{
  44 00039     \textcolor{keyword}{const} \textcolor{keywordtype}{char} *pos;
  45 00040     pos = strchr(Law\_and\_Order, c);
  46 00041     \textcolor{keywordflow}{if} (pos==NULL) code=0;
  47 00042     \textcolor{keywordflow}{else} code = (int) (pos-Law\_and\_Order);
  48 00043     \textcolor{keywordflow}{if} (code>5) code = 0;
  49 00044     \textcolor{keywordflow}{if} (code>4) code--; \textcolor{comment}{/* make T and U equivalent */}
  50 00045   \}
  51 00046   \textcolor{keywordflow}{return} code;
  52 00047 \}
  53 00048
  54 00049 \textcolor{comment}{/*@+boolint +charint@*/}
  55 00050 \textcolor{comment}{/*@null@*/}
  56 00051 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} *\hyperlink{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{nonstandards};
  57 00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{void}   \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]);
  58 00053 \textcolor{keyword}{static} \textcolor{keywordtype}{void} make\_pair\_matrix(\textcolor{keywordtype}{void})
  59 00054 \{
  60 00055    \textcolor{keywordtype}{int} i,j;
  61 00056
  62 00057    \textcolor{keywordflow}{if} (energy\_set==0) \{
  63 00058       \textcolor{keywordflow}{for} (i=0; i<5; i++) alias[i] = (\textcolor{keywordtype}{short}) i;
  64 00059       alias[5] = 3; \textcolor{comment}{/* X <-> G */}
  65 00060       alias[6] = 2; \textcolor{comment}{/* K <-> C */}
  66 00061       alias[7] = 0; \textcolor{comment}{/* I <-> default base '@' */}
  67 00062       \textcolor{keywordflow}{for} (i=0; i<NBASES; i++) \{
  68 00063           \textcolor{keywordflow}{for} (j=0; j<NBASES; j++)
  69 00064             pair[i][j] = BP\_pair[i][j];
  70 00065       \}
  71 00066       \textcolor{keywordflow}{if} (noGU) pair[3][4] = pair[4][3] =0;
  72 00067       \textcolor{keywordflow}{if} (nonstandards!=NULL) \{  \textcolor{comment}{/* allow nonstandard bp's */}
  73 00068          \textcolor{keywordflow}{for} (i=0; i<(int)strlen(nonstandards); i+=2)
  74 00069             pair[encode\_char(nonstandards[i])]
  75 00070               [encode\_char(nonstandards[i+1])]=7;
  76 00071       \}
  77 00072       \textcolor{keywordflow}{for} (i=0; i<NBASES; i++) \{
  78 00073           \textcolor{keywordflow}{for} (j=0; j<NBASES; j++)
  79 00074            rtype[pair[i][j]] = pair[j][i];
  80 00075       \}
  81 00076    \} \textcolor{keywordflow}{else} \{
  82 00077       \textcolor{keywordflow}{for} (i=0; i<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
  83 00078          \textcolor{keywordflow}{for} (j=0; j<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; j++)
  84 00079             pair[i][j] = 0;
  85 00080       \}
  86 00081       \textcolor{keywordflow}{if} (energy\_set==1) \{
  87 00082          \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA};) \{
  88 00083             alias[i++] = 3;  \textcolor{comment}{/* A <-> G */}
  89 00084             alias[i++] = 2;  \textcolor{comment}{/* B <-> C */}
  90 00085          \}
  91 00086          \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
  92 00087             pair[i][i+1] = 2;    \textcolor{comment}{/* AB <-> GC */}
  93 00088             i++;
  94 00089             pair[i][i-1] = 1;    \textcolor{comment}{/* BA <-> CG */}
  95 00090          \}
  96 00091       \}
  97 00092       \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (energy\_set==2) \{
  98 00093         \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA};) \{
  99 00094             alias[i++] = 1;  \textcolor{comment}{/* A <-> A*/}
 100 00095             alias[i++] = 4;  \textcolor{comment}{/* B <-> U */}
 101 00096          \}
 102 00097          \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
 103 00098             pair[i][i+1] = 5;    \textcolor{comment}{/* AB <-> AU */}
 104 00099             i++;
 105 00100             pair[i][i-1] = 6;    \textcolor{comment}{/* BA <-> UA */}
 106 00101          \}
 107 00102       \}
 108 00103       \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (energy\_set==3) \{
 109 00104         \textcolor{keywordflow}{for} (i=1; i<MAXALPHA-2; ) \{
 110 00105           alias[i++] = 3;  \textcolor{comment}{/* A <-> G */}
 111 00106           alias[i++] = 2;  \textcolor{comment}{/* B <-> C */}
 112 00107           alias[i++] = 1;  \textcolor{comment}{/* C <-> A */}
 113 00108           alias[i++] = 4;  \textcolor{comment}{/* D <-> U */}
 114 00109         \}
 115 00110         \textcolor{keywordflow}{for} (i=1; i<MAXALPHA-2; i++) \{
 116 00111           pair[i][i+1] = 2;    \textcolor{comment}{/* AB <-> GC */}
 117 00112           i++;
 118 00113           pair[i][i-1] = 1;    \textcolor{comment}{/* BA <-> CG */}
 119 00114           i++;
 120 00115           pair[i][i+1] = 5;    \textcolor{comment}{/* CD <-> AU */}
 121 00116           i++;
 122 00117           pair[i][i-1] = 6;    \textcolor{comment}{/* DC <-> UA */}
 123 00118         \}
 124 00119       \}
 125 00120       \textcolor{keywordflow}{else} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{stringliteral}{"What energy\_set are YOU using??"});
 126 00121       \textcolor{keywordflow}{for} (i=0; i<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
 127 00122         \textcolor{keywordflow}{for} (j=0; j<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; j++)
 128 00123           rtype[pair[i][j]] = pair[j][i];
 129 00124       \}
 130 00125    \}
 131 00126 \}
 132 00127
 133 00128 \textcolor{keyword}{static} \textcolor{keywordtype}{short} *encode\_sequence(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, \textcolor{keywordtype}{short} how)\{
 134 00129   \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} i,l = (\textcolor{keywordtype}{unsigned} int)strlen(sequence);
 135 00130   \textcolor{keywordtype}{short}         *S = (\textcolor{keywordtype}{short} *) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{short})*(l+2));
 136 00131
 137 00132   \textcolor{keywordflow}{switch}(how)\{
 138 00133     \textcolor{comment}{/* standard encoding as always used for S */}
 139 00134     \textcolor{keywordflow}{case} 0:   \textcolor{keywordflow}{for}(i=1; i<=l; i++) \textcolor{comment}{/* make numerical encoding of sequence */}
 140 00135                 S[i]= (\textcolor{keywordtype}{short}) encode\_char(toupper(sequence[i-1]));
 141 00136               S[l+1] = S[1];
 142 00137               S[0] = (short) l;
 143 00138               \textcolor{keywordflow}{break};
 144 00139     \textcolor{comment}{/* encoding for mismatches of nostandard bases (normally used for S1) */}
 145 00140     \textcolor{keywordflow}{case} 1:   \textcolor{keywordflow}{for}(i=1; i<=l; i++)
 146 00141                 S[i] = alias[(\textcolor{keywordtype}{short}) encode\_char(toupper(sequence[i-1]))];
 147 00142               S[l+1] = S[1];
 148 00143               S[0] = S[l];
 149 00144               \textcolor{keywordflow}{break};
 150 00145   \}
 151 00146
 152 00147   \textcolor{keywordflow}{return} S;
 153 00148 \}
 154 \end{DoxyCode}