--- /dev/null
+\hypertarget{pair__mat_8h}{\section{pair\-\_\-mat.\-h}
+\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}}
+}
+
+\begin{DoxyCode}
+00001 \textcolor{preprocessor}{#include <ctype.h>}
+00002 \textcolor{preprocessor}{#include "\hyperlink{utils_8h}{utils.h}"}
+00003 \textcolor{preprocessor}{#include "\hyperlink{fold__vars_8h}{fold\_vars.h}"}
+00004
+00005 \textcolor{preprocessor}{#define NBASES 8}
+00006 \textcolor{preprocessor}{}\textcolor{comment}{/*@notnull@*/}
+00007
+00008 \textcolor{keyword}{static} \textcolor{keyword}{const} \textcolor{keywordtype}{char} Law\_and\_Order[] = \textcolor{stringliteral}{"\_ACGUTXKI"};
+00009 \textcolor{keyword}{static} \textcolor{keywordtype}{int} BP\_pair[NBASES][NBASES]=
+00010 \textcolor{comment}{/* \_ A C G U X K I */}
+00011 \{\{ 0, 0, 0, 0, 0, 0, 0, 0\},
+00012 \{ 0, 0, 0, 0, 5, 0, 0, 5\},
+00013 \{ 0, 0, 0, 1, 0, 0, 0, 0\},
+00014 \{ 0, 0, 2, 0, 3, 0, 0, 0\},
+00015 \{ 0, 6, 0, 4, 0, 0, 0, 6\},
+00016 \{ 0, 0, 0, 0, 0, 0, 2, 0\},
+00017 \{ 0, 0, 0, 0, 0, 1, 0, 0\},
+00018 \{ 0, 6, 0, 0, 5, 0, 0, 0\}\};
+00019
+00020 \textcolor{preprocessor}{#define MAXALPHA 20 }\textcolor{comment}{/* maximal length of alphabet */}\textcolor{preprocessor}{}
+00021 \textcolor{preprocessor}{}
+00022 \textcolor{keyword}{static} \textcolor{keywordtype}{short} alias[\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1];
+00023 \textcolor{keyword}{static} \textcolor{keywordtype}{int} pair[\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1][\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}+1];
+00024 \textcolor{comment}{/* rtype[pair[i][j]]:=pair[j][i] */}
+00025 \textcolor{keyword}{static} \textcolor{keywordtype}{int} rtype[8] = \{0, 2, 1, 4, 3, 6, 5, 7\};
+00026
+00027 \textcolor{preprocessor}{#ifdef \_OPENMP}
+00028 \textcolor{preprocessor}{}\textcolor{preprocessor}{#pragma omp threadprivate(Law\_and\_Order, BP\_pair, alias, pair, rtype)}
+00029 \textcolor{preprocessor}{}\textcolor{preprocessor}{#endif}
+00030 \textcolor{preprocessor}{}
+00031 \textcolor{comment}{/* for backward compatibility */}
+00032 \textcolor{preprocessor}{#define ENCODE(c) encode\_char(c)}
+00033 \textcolor{preprocessor}{}
+00034 \textcolor{keyword}{static} \textcolor{keywordtype}{int} encode\_char(\textcolor{keywordtype}{char} c) \{
+00035 \textcolor{comment}{/* return numerical representation of base used e.g. in pair[][] */}
+00036 \textcolor{keywordtype}{int} code;
+00037 \textcolor{keywordflow}{if} (energy\_set>0) code = (int) (c-\textcolor{charliteral}{'A'})+1;
+00038 \textcolor{keywordflow}{else} \{
+00039 \textcolor{keyword}{const} \textcolor{keywordtype}{char} *pos;
+00040 pos = strchr(Law\_and\_Order, c);
+00041 \textcolor{keywordflow}{if} (pos==NULL) code=0;
+00042 \textcolor{keywordflow}{else} code = (int) (pos-Law\_and\_Order);
+00043 \textcolor{keywordflow}{if} (code>5) code = 0;
+00044 \textcolor{keywordflow}{if} (code>4) code--; \textcolor{comment}{/* make T and U equivalent */}
+00045 \}
+00046 \textcolor{keywordflow}{return} code;
+00047 \}
+00048
+00049 \textcolor{comment}{/*@+boolint +charint@*/}
+00050 \textcolor{comment}{/*@null@*/}
+00051 \textcolor{keyword}{extern} \textcolor{keywordtype}{char} *\hyperlink{fold__vars_8h_a2695d91cc535d09c2eae5c3884e2ec64}{nonstandards};
+00052 \textcolor{keyword}{extern} \textcolor{keywordtype}{void} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{keyword}{const} \textcolor{keywordtype}{char} message[]);
+00053 \textcolor{keyword}{static} \textcolor{keywordtype}{void} make\_pair\_matrix(\textcolor{keywordtype}{void})
+00054 \{
+00055 \textcolor{keywordtype}{int} i,j;
+00056
+00057 \textcolor{keywordflow}{if} (energy\_set==0) \{
+00058 \textcolor{keywordflow}{for} (i=0; i<5; i++) alias[i] = (\textcolor{keywordtype}{short}) i;
+00059 alias[5] = 3; \textcolor{comment}{/* X <-> G */}
+00060 alias[6] = 2; \textcolor{comment}{/* K <-> C */}
+00061 alias[7] = 0; \textcolor{comment}{/* I <-> default base '@' */}
+00062 \textcolor{keywordflow}{for} (i=0; i<NBASES; i++) \{
+00063 \textcolor{keywordflow}{for} (j=0; j<NBASES; j++)
+00064 pair[i][j] = BP\_pair[i][j];
+00065 \}
+00066 \textcolor{keywordflow}{if} (noGU) pair[3][4] = pair[4][3] =0;
+00067 \textcolor{keywordflow}{if} (nonstandards!=NULL) \{ \textcolor{comment}{/* allow nonstandard bp's */}
+00068 \textcolor{keywordflow}{for} (i=0; i<(int)strlen(nonstandards); i+=2)
+00069 pair[encode\_char(nonstandards[i])]
+00070 [encode\_char(nonstandards[i+1])]=7;
+00071 \}
+00072 \textcolor{keywordflow}{for} (i=0; i<NBASES; i++) \{
+00073 \textcolor{keywordflow}{for} (j=0; j<NBASES; j++)
+00074 rtype[pair[i][j]] = pair[j][i];
+00075 \}
+00076 \} \textcolor{keywordflow}{else} \{
+00077 \textcolor{keywordflow}{for} (i=0; i<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
+00078 \textcolor{keywordflow}{for} (j=0; j<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; j++)
+00079 pair[i][j] = 0;
+00080 \}
+00081 \textcolor{keywordflow}{if} (energy\_set==1) \{
+00082 \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA};) \{
+00083 alias[i++] = 3; \textcolor{comment}{/* A <-> G */}
+00084 alias[i++] = 2; \textcolor{comment}{/* B <-> C */}
+00085 \}
+00086 \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
+00087 pair[i][i+1] = 2; \textcolor{comment}{/* AB <-> GC */}
+00088 i++;
+00089 pair[i][i-1] = 1; \textcolor{comment}{/* BA <-> CG */}
+00090 \}
+00091 \}
+00092 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (energy\_set==2) \{
+00093 \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA};) \{
+00094 alias[i++] = 1; \textcolor{comment}{/* A <-> A*/}
+00095 alias[i++] = 4; \textcolor{comment}{/* B <-> U */}
+00096 \}
+00097 \textcolor{keywordflow}{for} (i=1; i<\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
+00098 pair[i][i+1] = 5; \textcolor{comment}{/* AB <-> AU */}
+00099 i++;
+00100 pair[i][i-1] = 6; \textcolor{comment}{/* BA <-> UA */}
+00101 \}
+00102 \}
+00103 \textcolor{keywordflow}{else} \textcolor{keywordflow}{if} (energy\_set==3) \{
+00104 \textcolor{keywordflow}{for} (i=1; i<MAXALPHA-2; ) \{
+00105 alias[i++] = 3; \textcolor{comment}{/* A <-> G */}
+00106 alias[i++] = 2; \textcolor{comment}{/* B <-> C */}
+00107 alias[i++] = 1; \textcolor{comment}{/* C <-> A */}
+00108 alias[i++] = 4; \textcolor{comment}{/* D <-> U */}
+00109 \}
+00110 \textcolor{keywordflow}{for} (i=1; i<MAXALPHA-2; i++) \{
+00111 pair[i][i+1] = 2; \textcolor{comment}{/* AB <-> GC */}
+00112 i++;
+00113 pair[i][i-1] = 1; \textcolor{comment}{/* BA <-> CG */}
+00114 i++;
+00115 pair[i][i+1] = 5; \textcolor{comment}{/* CD <-> AU */}
+00116 i++;
+00117 pair[i][i-1] = 6; \textcolor{comment}{/* DC <-> UA */}
+00118 \}
+00119 \}
+00120 \textcolor{keywordflow}{else} \hyperlink{utils_8h_a127ce946e56b5a5773781cabe68e38c5}{nrerror}(\textcolor{stringliteral}{"What energy\_set are YOU using??"});
+00121 \textcolor{keywordflow}{for} (i=0; i<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; i++) \{
+00122 \textcolor{keywordflow}{for} (j=0; j<=\hyperlink{data__structures_8h_a05a5ffe718aa431d97419a12fb082379}{MAXALPHA}; j++)
+00123 rtype[pair[i][j]] = pair[j][i];
+00124 \}
+00125 \}
+00126 \}
+00127
+00128 \textcolor{keyword}{static} \textcolor{keywordtype}{short} *encode\_sequence(\textcolor{keyword}{const} \textcolor{keywordtype}{char} *sequence, \textcolor{keywordtype}{short} how)\{
+00129 \textcolor{keywordtype}{unsigned} \textcolor{keywordtype}{int} i,l = (\textcolor{keywordtype}{unsigned} int)strlen(sequence);
+00130 \textcolor{keywordtype}{short} *S = (\textcolor{keywordtype}{short} *) \hyperlink{utils_8h_ad7e1e137b3bf1f7108933d302a7f0177}{space}(\textcolor{keyword}{sizeof}(\textcolor{keywordtype}{short})*(l+2));
+00131
+00132 \textcolor{keywordflow}{switch}(how)\{
+00133 \textcolor{comment}{/* standard encoding as always used for S */}
+00134 \textcolor{keywordflow}{case} 0: \textcolor{keywordflow}{for}(i=1; i<=l; i++) \textcolor{comment}{/* make numerical encoding of sequence */}
+00135 S[i]= (\textcolor{keywordtype}{short}) encode\_char(toupper(sequence[i-1]));
+00136 S[l+1] = S[1];
+00137 S[0] = (short) l;
+00138 \textcolor{keywordflow}{break};
+00139 \textcolor{comment}{/* encoding for mismatches of nostandard bases (normally used for S1) */}
+00140 \textcolor{keywordflow}{case} 1: \textcolor{keywordflow}{for}(i=1; i<=l; i++)
+00141 S[i] = alias[(\textcolor{keywordtype}{short}) encode\_char(toupper(sequence[i-1]))];
+00142 S[l+1] = S[1];
+00143 S[0] = S[l];
+00144 \textcolor{keywordflow}{break};
+00145 \}
+00146
+00147 \textcolor{keywordflow}{return} S;
+00148 \}
+\end{DoxyCode}
git://source.jalview.org / jabaws.git / blobdiff