X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2Fsrc%2FViennaRNA%2Fdoc%2FRNAlib-2.1.2.tag;h=2dfc5934b52023f0daa5a9eca1038b4034a7fbd8;hb=ecfc686151bf027d4deb3c7a7510861d35c51730;hp=68aee50579fd685f6e15abf569c531a450128071;hpb=b4ff3ef8dc5d197f41d83de832e94e3b45a5c12e;p=jabaws.git

diff --git a/binaries/src/ViennaRNA/doc/RNAlib-2.1.2.tag b/binaries/src/ViennaRNA/doc/RNAlib-2.1.2.tag
index 68aee50..2dfc593 100644
--- a/binaries/src/ViennaRNA/doc/RNAlib-2.1.2.tag
+++ b/binaries/src/ViennaRNA/doc/RNAlib-2.1.2.tag
@@ -1,8 +1,14 @@
-<?xml version='1.0' encoding='UTF-8' standalone='yes' ?>
+<?xml version='1.0' encoding='ISO-8859-1' standalone='yes' ?>
 <tagfile>
+  <compound kind="page">
+    <name>main</name>
+    <title>ViennaRNA Package core - RNAlib</title>
+    <filename>main</filename>
+    <docanchor file="main">mp_intro</docanchor>
+  </compound>
   <compound kind="file">
     <name>2Dfold.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>2Dfold_8h</filename>
     <member kind="function">
       <type>TwoDfold_vars *</type>
@@ -35,7 +41,7 @@
   </compound>
   <compound kind="file">
     <name>2Dpfold.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>2Dpfold_8h</filename>
     <member kind="function">
       <type>TwoDpfold_vars *</type>
@@ -82,7 +88,7 @@
   </compound>
   <compound kind="file">
     <name>alifold.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>alifold_8h</filename>
     <member kind="function">
       <type>void</type>
@@ -176,10 +182,10 @@
       <arglist>(const char **sequences, char *structure, plist **pl)</arglist>
     </member>
     <member kind="function">
-      <type>double *</type>
+      <type>FLT_OR_DBL *</type>
       <name>export_ali_bppm</name>
       <anchorfile>group__consensus__pf__fold.html</anchorfile>
-      <anchor>gadaaf83394216413505e48d913dbc1b4e</anchor>
+      <anchor>ga11b6ab8bd9be1821fea352b190a01cab</anchor>
       <arglist>(void)</arglist>
     </member>
     <member kind="function">
@@ -193,8 +199,8 @@
       <type>int</type>
       <name>get_alipf_arrays</name>
       <anchorfile>group__consensus__fold.html</anchorfile>
-      <anchor>ga0cc49457fd79eeb04d4a7f97c868b09b</anchor>
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+      <anchor>ga5349960075b1847720a2e9df021e2675</anchor>
+      <arglist>(short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)</arglist>
     </member>
     <member kind="variable">
       <type>double</type>
@@ -213,7 +219,7 @@
   </compound>
   <compound kind="file">
     <name>cofold.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>cofold_8h</filename>
     <member kind="function">
       <type>float</type>
@@ -288,7 +294,7 @@
   </compound>
   <compound kind="file">
     <name>convert_epars.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>convert__epars_8h</filename>
     <member kind="define">
       <type>#define</type>
@@ -454,7 +460,7 @@
   </compound>
   <compound kind="file">
     <name>data_structures.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>data__structures_8h</filename>
     <class kind="struct">plist</class>
     <class kind="struct">cpair</class>
@@ -504,7 +510,7 @@
   </compound>
   <compound kind="file">
     <name>dist_vars.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>dist__vars_8h</filename>
     <class kind="struct">Postorder_list</class>
     <class kind="struct">Tree</class>
@@ -533,17 +539,17 @@
   </compound>
   <compound kind="file">
     <name>duplex.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>duplex_8h</filename>
   </compound>
   <compound kind="file">
     <name>edit_cost.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>edit__cost_8h</filename>
   </compound>
   <compound kind="file">
     <name>energy_const.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>energy__const_8h</filename>
     <member kind="define">
       <type>#define</type>
@@ -604,7 +610,7 @@
   </compound>
   <compound kind="file">
     <name>findpath.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>findpath_8h</filename>
     <member kind="function">
       <type>int</type>
@@ -630,7 +636,7 @@
   </compound>
   <compound kind="file">
     <name>fold.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>fold_8h</filename>
     <member kind="function">
       <type>float</type>
@@ -824,7 +830,7 @@
   </compound>
   <compound kind="file">
     <name>fold_vars.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>fold__vars_8h</filename>
     <member kind="function">
       <type>void</type>
@@ -1004,7 +1010,7 @@
   </compound>
   <compound kind="file">
     <name>gquad.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>gquad_8h</filename>
     <member kind="function">
       <type>int *</type>
@@ -1037,7 +1043,7 @@
   </compound>
   <compound kind="file">
     <name>inverse.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>inverse_8h</filename>
     <member kind="function">
       <type>float</type>
@@ -1084,7 +1090,7 @@
   </compound>
   <compound kind="file">
     <name>Lfold.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>Lfold_8h</filename>
     <member kind="function">
       <type>float</type>
@@ -1110,7 +1116,7 @@
   </compound>
   <compound kind="file">
     <name>loop_energies.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>loop__energies_8h</filename>
     <member kind="function">
       <type>PRIVATE int</type>
@@ -1157,7 +1163,7 @@
   </compound>
   <compound kind="file">
     <name>LPfold.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>LPfold_8h</filename>
     <member kind="function">
       <type>void</type>
@@ -1204,7 +1210,7 @@
   </compound>
   <compound kind="file">
     <name>MEA.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>MEA_8h</filename>
     <member kind="function">
       <type>float</type>
@@ -1216,17 +1222,17 @@
   </compound>
   <compound kind="file">
     <name>mm.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>mm_8h</filename>
   </compound>
   <compound kind="file">
     <name>naview.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>naview_8h</filename>
   </compound>
   <compound kind="file">
     <name>params.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>params_8h</filename>
     <member kind="function">
       <type>paramT *</type>
@@ -1271,16 +1277,16 @@
       <arglist>(unsigned int n_seq)</arglist>
     </member>
     <member kind="function">
-      <type>PUBLIC pf_paramT *</type>
+      <type>pf_paramT *</type>
       <name>get_boltzmann_factors_ali</name>
       <anchorfile>group__energy__parameters.html</anchorfile>
-      <anchor>gaaa049a8c9f1c2ed4398cb1b5a3d65a66</anchor>
+      <anchor>gaf0c74574b40f2778556535bf9d382828</anchor>
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   </compound>
   <compound kind="file">
     <name>part_func.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>part__func_8h</filename>
     <member kind="function">
       <type>float</type>
@@ -1453,7 +1459,7 @@
   </compound>
   <compound kind="file">
     <name>part_func_co.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>part__func__co_8h</filename>
     <member kind="function">
       <type>cofoldF</type>
@@ -1542,7 +1548,7 @@
   </compound>
   <compound kind="file">
     <name>part_func_up.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>part__func__up_8h</filename>
     <member kind="function">
       <type>pu_contrib *</type>
@@ -1575,7 +1581,7 @@
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   <compound kind="file">
     <name>plot_layouts.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>plot__layouts_8h</filename>
     <member kind="define">
       <type>#define</type>
@@ -1622,7 +1628,7 @@
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   <compound kind="file">
     <name>profiledist.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>profiledist_8h</filename>
     <member kind="function">
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@@ -1662,7 +1668,7 @@
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   <compound kind="file">
     <name>PS_dot.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>PS__dot_8h</filename>
     <member kind="function">
       <type>int</type>
@@ -1730,7 +1736,7 @@
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   <compound kind="file">
     <name>read_epars.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
     <filename>read__epars_8h</filename>
     <member kind="function">
       <type>void</type>
@@ -1749,7 +1755,7 @@
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   <compound kind="file">
     <name>RNAstruct.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
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     <member kind="function">
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   <compound kind="file">
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-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
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     <member kind="function">
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   <compound kind="file">
     <name>subopt.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
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     <member kind="function">
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   <compound kind="file">
     <name>treedist.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
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   <compound kind="file">
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-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/H/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/H/</path>
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     <member kind="define">
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@@ -2404,12 +2410,12 @@
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   <compound kind="file">
     <name>1.8.4_epars.h</name>
-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/lib/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/</path>
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   <compound kind="file">
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-    <path>/home/mescalin/ronny/public_html/programs/ViennaRNA/lib/</path>
+    <path>/homes/fmmarquesmadeira/Projects/jabaws/binaries/src/ViennaRNA/lib/</path>
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   <compound kind="page">
@@ -2421,24 +2427,19 @@
     <name>mp_utils</name>
     <title>Utilities - Odds and Ends</title>
     <filename>mp_utils</filename>
+    <docanchor file="mp_utils">utils_struc</docanchor>
+    <docanchor file="mp_utils">utils_dot</docanchor>
     <docanchor file="mp_utils">toc</docanchor>
+    <docanchor file="mp_utils">utils_misc</docanchor>
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   <compound kind="page">
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     <title>Example - A Small Example Program</title>
     <filename>mp_example</filename>
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-    <title>Bibliographic References</title>
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     <title>RNA Secondary Structure Folding</title>
@@ -2509,7 +2510,6 @@
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     <member kind="function">
       <type>float</type>
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@@ -2619,7 +2619,6 @@
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     <subgroup>subopt_stochbt</subgroup>
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   <compound kind="group">
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@@ -2882,7 +2881,6 @@
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     <member kind="function">
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@@ -2929,8 +2927,8 @@
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+      <anchor>ga5349960075b1847720a2e9df021e2675</anchor>
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@@ -2999,10 +2997,10 @@
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+      <type>FLT_OR_DBL *</type>
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       <anchorfile>group__consensus__pf__fold.html</anchorfile>
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@@ -3025,7 +3023,6 @@
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@@ -3050,7 +3047,6 @@
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-    <file>LPfold.h</file>
     <member kind="function">
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@@ -3148,10 +3144,10 @@
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     <member kind="function">
-      <type>PUBLIC pf_paramT *</type>
+      <type>pf_paramT *</type>
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@@ -4318,75 +4314,4 @@
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