WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / RNAforester / src / rnafuncs.h

diff --git a/binaries/src/ViennaRNA/RNAforester/src/rnafuncs.h b/binaries/src/ViennaRNA/RNAforester/src/rnafuncs.h
new file mode 100644 (file)
index 0000000..2ff95ee
--- /dev/null
+++ b/binaries/src/ViennaRNA/RNAforester/src/rnafuncs.h
@@ -0,0 +1,68 @@
+#ifndef _RNA_FUNCS_H
+#define _RNA_FUNCS_H
+
+#include <deque>
+#include <list>
+#include <string>
+
+#include "types.h"
+#include "rnaforester_options.h"
+#include "rna_profile_alignment.h"
+
+#ifdef HAVE_LIBXMLPLUSPLUS
+#ifdef HAVE_LIBXML2
+#include <libxml++/libxml++.h>
+#endif
+#endif
+
+using namespace std;
+       
+class RNAFuncs
+{
+ public:
+  struct SquigglePlotOptions
+  {
+         bool hideBaseNumbers;
+         Uint baseNumInterval;
+         bool greyColors;
+         bool generatePNG;
+         bool generateJPG;
+          bool generateFIG;
+         double scale;
+  };
+
+  typedef struct AddXmlInfos {
+    map<int,string> idmapping;
+    map<int,string> comments;
+    map<int,string> descriptions;
+    map<int,string> names;
+    map<int,string> synonyms;
+    Uint xbasepos,ybasepos;
+    bool xmlInput;
+  };
+
+  static bool isRNAString(const string &str);
+  static bool isViennaString(const string &str, Ulong &basePairCount, Ulong &maxDepth);
+  static void drawRNAStructure(const string &seq, const string &structure, const string &filename_prefix, const string &structname, const list<pair<Uint,Uint> > &regions, const SquigglePlotOptions &options);
+  static void drawRNAAlignment(const string &structure, const string &altStructure,  const string &seq1, const string &seq2, const string &strname1, const string &strname2, const string &filename_prefix, const bool atX, const SquigglePlotOptions &options);
+  static void generateRNAAlignmentXML(const string &structure, const string &altStructure, const string &seq1, const string &seq2, const string &strname1, const string &strname2, ostream &s);
+  static void printAli(const string &name1, const string &id2, const string &seq1, const string &seq2, const string &str1, const string &str3);
+  
+  static Uint treeSize(const string &viennaStr);
+       
+#ifdef HAVE_LIBXMLPLUSPLUS
+#ifdef HAVE_LIBXML2
+       static string getXSDURL();
+       static void printMAliXML(deque<pair<double,RNAProfileAlignment*> > &resultList, const RNAforesterOptions &options,double &minPairProb,AddXmlInfos &xmlInfos,const string &outputFile);
+       static void printPAliXML(const string &id1, const string &name2, const string &seq1, const string &seq2, const string &str1, const string &str3, double &score, const RNAforesterOptions &options,AddXmlInfos &xmlInfos,const string &outputFile);
+       static void printMapping(map<int,string> &mapping);
+#endif 
+#endif
+       static string UpperCase(const string &str);
+};
+
+#endif
+
+
+
+