+\label{deprecated__deprecated000008}
+\hypertarget{deprecated__deprecated000008}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\_\-pair} ]Do not use this variable anymore!
+\end{DoxyDescription}
-\begin{DoxyRefList}
-\item[\label{deprecated__deprecated000008}%
-\hypertarget{deprecated__deprecated000008}{}%
-Global \hyperlink{fold__vars_8h_a0244a629b5ab4f58b77590c3dfd130dc}{base\-\_\-pair} ]Do not use this variable anymore!
-\item[\label{deprecated__deprecated000012}%
-\hypertarget{deprecated__deprecated000012}{}%
-Global \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid} (int length, double $\ast$dist)]This function is deprecated and should not be used anymore as it is not threadsafe!
-\item[\label{deprecated__deprecated000007}%
-\hypertarget{deprecated__deprecated000007}{}%
-Global \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\-\_\-of\-\_\-circ\-\_\-struct} (const char $\ast$string, const char $\ast$structure)]This function is deprecated and should not be used in future programs Use \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\-\_\-of\-\_\-circ\-\_\-structure()} instead!
-\item[\label{deprecated__deprecated000005}%
-\hypertarget{deprecated__deprecated000005}{}%
-Global \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\-\_\-of\-\_\-struct} (const char $\ast$string, const char $\ast$structure)]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\-\_\-of\-\_\-structure()} instead!
-\item[\label{deprecated__deprecated000006}%
-\hypertarget{deprecated__deprecated000006}{}%
-Global \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\-\_\-of\-\_\-struct\-\_\-pt} (const char $\ast$string, short $\ast$ptable, short $\ast$s, short $\ast$s1)]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\-\_\-of\-\_\-structure\-\_\-pt()} instead!
-\item[\label{deprecated__deprecated000015}%
-\hypertarget{deprecated__deprecated000015}{}%
-Global \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{exp\-Hairpin\-Energy} (int u, int type, short si1, short sj1, const char $\ast$string)]Use \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp\-\_\-\-E\-\_\-\-Hairpin()} from \hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h} instead
-\item[\label{deprecated__deprecated000014}%
-\hypertarget{deprecated__deprecated000014}{}%
-Global \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{exp\-Loop\-Energy} (int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1)]Use \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp\-\_\-\-E\-\_\-\-Int\-Loop()} from \hyperlink{loop__energies_8h}{loop\-\_\-energies.\-h} instead
-\item[\label{deprecated__deprecated000016}%
-\hypertarget{deprecated__deprecated000016}{}%
-Global \hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\-\_\-plist} (struct plist $\ast$pl, int length, double cut\-\_\-off)]\{ This function is deprecated and will be removed soon!\} use \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\-\_\-plist\-\_\-from\-\_\-pr()} instead!
-\item[\label{deprecated__deprecated000003}%
-\hypertarget{deprecated__deprecated000003}{}%
-Global \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{Hairpin\-E} (int size, int type, int si1, int sj1, const char $\ast$string)]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\-\_\-\-Hairpin()} instead!\}
-\item[\label{deprecated__deprecated000010}%
-\hypertarget{deprecated__deprecated000010}{}%
-Global \hyperlink{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{iindx} ]Do not use this variable anymore!
-\item[\label{deprecated__deprecated000017}%
-\hypertarget{deprecated__deprecated000017}{}%
-Global \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\-\_\-co\-\_\-pf\-\_\-fold} (int length)]\{ This function is deprecated and will be removed soon!\}
-\item[\label{deprecated__deprecated000011}%
-\hypertarget{deprecated__deprecated000011}{}%
-Global \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\-\_\-pf\-\_\-fold} (int length)]This function is obsolete and will be removed soon!
-\item[\label{deprecated__deprecated000001}%
-\hypertarget{deprecated__deprecated000001}{}%
-Global \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize\-\_\-cofold} (int length)]\{This function is obsolete and will be removed soon!\}
-\item[\label{deprecated__deprecated000004}%
-\hypertarget{deprecated__deprecated000004}{}%
-Global \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\-\_\-fold} (int length)]\{This function is deprecated and will be removed soon!\}
-\item[\label{deprecated__deprecated000002}%
-\hypertarget{deprecated__deprecated000002}{}%
-Global \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{Loop\-Energy} (int n1, int n2, int type, int type\-\_\-2, int si1, int sj1, int sp1, int sq1)]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\-\_\-\-Int\-Loop()} instead!\}
-\item[\label{deprecated__deprecated000018}%
-\hypertarget{deprecated__deprecated000018}{}%
-Global \hyperlink{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{Make\-\_\-bp\-\_\-profile} (int length)]This function is deprecated and will be removed soon! See \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\-\_\-bp\-\_\-profile\-\_\-bppm()} for a replacement
-\item[\label{deprecated__deprecated000013}%
-\hypertarget{deprecated__deprecated000013}{}%
-Global \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\-\_\-bp\-\_\-dist} (int length)]This function is not threadsafe and should not be used anymore. Use \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\-\_\-bp\-\_\-distance()} instead!
-\item[\label{deprecated__deprecated000009}%
-\hypertarget{deprecated__deprecated000009}{}%
-Global \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr} ]Do not use this variable anymore!
-\item[\label{deprecated__deprecated000019}%
-\hypertarget{deprecated__deprecated000019}{}%
-Global \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{P\-S\-\_\-dot\-\_\-plot} (char $\ast$string, char $\ast$file)]This function is deprecated and will be removed soon! Use \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{P\-S\-\_\-dot\-\_\-plot\-\_\-list()} instead!
-\end{DoxyRefList}
\ No newline at end of file
+\label{deprecated__deprecated000012}
+\hypertarget{deprecated__deprecated000012}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{part__func_8h_ae89a63bd83e75a80b2ba36d20b31ce81}{centroid} ]This function is deprecated and should not be used anymore as it is not threadsafe!
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000007}
+\hypertarget{deprecated__deprecated000007}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold_8h_a657222e2758c46bf13b416ef3032e417}{energy\_\-of\_\-circ\_\-struct} ]This function is deprecated and should not be used in future programs Use \hyperlink{group__eval_gaeb14f3664aec67fc03268ac75253f0f8}{energy\_\-of\_\-circ\_\-structure()} instead!
+
+
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000005}
+\hypertarget{deprecated__deprecated000005}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold_8h_ac2b37fea2145c94d925a3f33378ef87b}{energy\_\-of\_\-struct} ]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_gaf93986cb3cb29770ec9cca69c9fab8cf}{energy\_\-of\_\-structure()} instead!
+
+
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000006}
+\hypertarget{deprecated__deprecated000006}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold_8h_a27ce6f68512d43bf1fe14a06c9d76d5c}{energy\_\-of\_\-struct\_\-pt} ]This function is deprecated and should not be used in future programs! Use \hyperlink{group__eval_ga8831445966b761417e713360791299d8}{energy\_\-of\_\-structure\_\-pt()} instead!
+
+
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000015}
+\hypertarget{deprecated__deprecated000015}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{part__func_8h_a7b6ab474cc80accc48010ccfcc59f96b}{expHairpinEnergy} ]Use \hyperlink{loop__energies_8h_a0e128184bb097dc2da33706f33b555a6}{exp\_\-E\_\-Hairpin()} from \hyperlink{loop__energies_8h}{loop\_\-energies.h} instead
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000014}
+\hypertarget{deprecated__deprecated000014}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{part__func_8h_a68ba6f3a48e08ca131ab54621ce3a2d7}{expLoopEnergy} ]Use \hyperlink{loop__energies_8h_aa5e98e524e2a41e290b942b09544bc9e}{exp\_\-E\_\-IntLoop()} from \hyperlink{loop__energies_8h}{loop\_\-energies.h} instead
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000016}
+\hypertarget{deprecated__deprecated000016}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{part__func__co_8h_a334de3c96e2186abfbdc0eaea6d08b14}{get\_\-plist} ]\{ This function is deprecated and will be removed soon!\} use \hyperlink{group__pf__fold_ga03e15e831a31b1154855ab47edbdb019}{assign\_\-plist\_\-from\_\-pr()} instead!
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000003}
+\hypertarget{deprecated__deprecated000003}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold_8h_ab327ce11972f5ac069d52c8dedfdb700}{HairpinE} ]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_aa362183cf6db89a10cdb0f5c4bd180c6}{E\_\-Hairpin()} instead!\}
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000010}
+\hypertarget{deprecated__deprecated000010}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold__vars_8h_a92089ae3a51b5d75a14ce9cc29cc8317}{iindx} ]Do not use this variable anymore!
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000017}
+\hypertarget{deprecated__deprecated000017}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{part__func__co_8h_aa12dda9dd6179cdd22bcce87c0682c07}{init\_\-co\_\-pf\_\-fold} ]\{ This function is deprecated and will be removed soon!\}
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000011}
+\hypertarget{deprecated__deprecated000011}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{part__func_8h_a15176e23eceeff8c7d14eabcfec8a2af}{init\_\-pf\_\-fold} ]This function is obsolete and will be removed soon!
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000001}
+\hypertarget{deprecated__deprecated000001}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{cofold_8h_afee0c32208aa2ac97338b6e3fbad7fa5}{initialize\_\-cofold} ]\{This function is obsolete and will be removed soon!\}
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000004}
+\hypertarget{deprecated__deprecated000004}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold_8h_ac3f0a28d9cb609d388b155445073fd20}{initialize\_\-fold} ]\{This function is deprecated and will be removed soon!\}
+
+
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000002}
+\hypertarget{deprecated__deprecated000002}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold_8h_a2163034a25c6115d894b199e97e03f6c}{LoopEnergy} ]\{This function is deprecated and will be removed soon. Use \hyperlink{loop__energies_8h_a3e5ad89f451254b1fe366d77aa8ff7bd}{E\_\-IntLoop()} instead!\}
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000018}
+\hypertarget{deprecated__deprecated000018}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{profiledist_8h_a904c7eaf4a2413567c00ac4891749d18}{Make\_\-bp\_\-profile} ]This function is deprecated and will be removed soon! See \hyperlink{profiledist_8h_a8822fd5268be115c6e6cdc92009436cc}{Make\_\-bp\_\-profile\_\-bppm()} for a replacement
+
+
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000013}
+\hypertarget{deprecated__deprecated000013}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{part__func_8h_ae9556ba7ded44fe2321b6f67c3fc02a3}{mean\_\-bp\_\-dist} ]This function is not threadsafe and should not be used anymore. Use \hyperlink{group__pf__fold_ga79cbc375af65f11609feb6b055269e7d}{mean\_\-bp\_\-distance()} instead!
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000009}
+\hypertarget{deprecated__deprecated000009}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{fold__vars_8h_a0f5757427fd5f2f79d6fca0081cd5a52}{pr} ]Do not use this variable anymore!
+\end{DoxyDescription}
+
+\label{deprecated__deprecated000019}
+\hypertarget{deprecated__deprecated000019}{}
+
+\begin{DoxyDescription}
+\item[Global \hyperlink{PS__dot_8h_a689a97a7e3b8a2df14728b8204d9d57b}{PS\_\-dot\_\-plot} ]This function is deprecated and will be removed soon! Use \hyperlink{PS__dot_8h_a00ea223b5cf02eb2faae5ff29f0d5e12}{PS\_\-dot\_\-plot\_\-list()} instead!
+\end{DoxyDescription}
\ No newline at end of file
git://source.jalview.org / jabaws.git / blobdiff