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

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

diff --git a/binaries/src/ViennaRNA/RNAforester/src/rna_profile_alignment.h b/binaries/src/ViennaRNA/RNAforester/src/rna_profile_alignment.h
new file mode 100644 (file)
index 0000000..3981d81
--- /dev/null
+++ b/binaries/src/ViennaRNA/RNAforester/src/rna_profile_alignment.h
@@ -0,0 +1,147 @@
+/*
+  Copyright by Matthias Hoechsmann (C) 2002-2004
+  =====================================                                   
+  You may use, copy and distribute this file freely as long as you
+  - do not change the file,
+  - leave this copyright notice in the file,
+  - do not make any profit with the distribution of this file
+  - give credit where credit is due
+  You are not allowed to copy or distribute this file otherwise
+  The commercial usage and distribution of this file is prohibited
+  Please report bugs and suggestions to <mhoechsm@TechFak.Uni-Bielefeld.DE>
+*/
+
+#ifndef _RNA_PROFILE_ALIGNMENT_H
+#define _RNA_PROFILE_ALIGNMENT_H
+
+#include <deque>
+#include <iostream>
+#include <map>
+
+#include "alignment.h"
+#include "matrix.h"
+#include "ppforestali.h"
+#include "rna_algebra.h"
+#include "types.h"
+
+//#include "alignment.t.cpp"
+
+using namespace std;
+
+class RNAProfileAlignment
+       : public PPForestAli<RNA_Alphabet_Profile,RNA_Alphabet_Profile>
+{
+ public:
+  //  typedef typename PPForestAli<RNA_Alphabet_Profile,RNA_Alphabet_Profile>::size_type size_type;
+
+  struct SquigglePlotOptions
+  {
+    bool hideBaseNumbers;
+    Uint baseNumInterval;
+    bool greyColors;
+    bool mostLikelySequence;
+    double minPairProb;        
+  };
+
+  struct BaseProbs
+  {
+    double a;
+    double c;
+    double g;
+    double u;
+    double gap;
+    double base;
+  };
+
+ private:
+  string m_name;
+  Uint m_numStructures;
+  Uint m_numStructuresX;
+  Uint m_numStructuresY;
+  deque<string> m_strNames;
+  bool hasSequence;
+
+  void makeRepLabel(size_type node, RNA_Alphabet_Profile a,  RNA_Alphabet_Profile b); 
+  void makeDelLabel(size_type node, RNA_Alphabet_Profile a); 
+  void makeInsLabel(size_type node, RNA_Alphabet_Profile b);
+  
+  void showLabel(ostream &s,RNA_Alphabet_Profile p) const;
+  void makeLabel(RNA_Alphabet_Profile &a,char c);
+
+  /** Build forest from structure, sequence pair. */
+  void buildForest(const string &baseStr, const string &viennaStr, bool use_bp_prob=false);
+
+  void getStructureAlignmentFromCSF(string &s, deque<double> &pairprop, double t,size_type i, size_type j) const; 
+  double bestPairs(size_type node) const;
+  void drawBaseCircles(int device_id,const BaseProbs &bp,double center_x,double center_y) const;
+  double getMlBaseFreq(const BaseProbs &baseprobs) const;
+  char getMlBase(const BaseProbs &bp) const;
+  void getSeqAli(string &seq,Uint row,Uint i,Uint j) const;
+  void getStructAli(string &str,Uint row) const;
+  void makePairTable(map<Uint,Uint> &pairs, Uint row) const;
+  void filterConsensus(string &structure, deque<double> &pairprob, deque<BaseProbs> &baseprobs, double minFreq) const; 
+  void addStrName(const string &strName) {m_strNames.push_back(strName);};
+
+  inline bool isBase(size_type node) const
+  {
+         if(label(node).p[ALPHA_PRO_BASE] > 0)
+                 return true;
+         else
+                 return false;
+  };
+
+  inline bool isPair(size_type node) const {return !isBase(node);};
+
+public:
+       RNAProfileAlignment(const string &baseStr, const string &viennaStr, const string &name);
+       RNAProfileAlignment(const string &baseStr, const string &constraint, const string &name, double t);
+       RNAProfileAlignment(const string &filename);
+
+       void printSeqAli() const;
+       deque<pair<string,string> > getSeqAli() const;
+       deque<string> getStrAli() const;
+       string getConsSeq() const;
+       string getConsStr(double minPairProb) const;
+       deque<double> getBaseProb() const;
+       //deque<pair<pair<int,int>,double> > getPairProb(double minPairProb);
+        void getPairProb(double &minPairProb, deque<pair<pair<int,int>,double> > &pairprobs);
+       void printStrAli() const;
+       void printConsensus(double minPairProb) const;
+       void printFastaAli(bool noStructure=false) const;
+
+       void squigglePlot(const string &filename, SquigglePlotOptions &options) const;
+       void getSequenceAlignment(deque<BaseProbs> &baseprob) const;
+       void getStructureAlignment(double t, string &s, deque<double> &pairprob) const;
+       string getName() const {return m_name;};
+       void setName(const string &name) {m_name=name;};
+       Uint getNumStructures() const {return m_numStructures;};
+       const deque<string>& getStrNames() const {return m_strNames;};
+       void addStrNames(const deque<string>& strNames);       
+       void save(const string &filename);
+       
+       RNAProfileAlignment(Uint numStructuresX,Uint numStructuresY) : 
+          PPForestAli<RNA_Alphabet_Profile,RNA_Alphabet_Profile>(),
+          m_numStructures(numStructuresX + numStructuresY),
+          m_numStructuresX(numStructuresX),
+          m_numStructuresY(numStructuresY){};
+};
+
+/*
+class Profile_RNA_Alignment: public Alignment<double,RNA_Alphabet_Profile,RNA_Alphabet_Profile>
+{
+ private:
+  string m_name;
+
+ public:
+  Profile_RNA_Alignment(const RNAProfileForest *ppfx, const RNAProfileForest *ppfy, const DoubleScoreProfileAlgebraType &alg)
+      : Alignment<double,RNA_Alphabet_Profile,RNA_Alphabet_Profile>((const PPForest<RNA_Alphabet_Profile>*)ppfx,(const PPForest<RNA_Alphabet_Profile>*)ppfy,alg)
+    {
+      m_name=ppfx->getName();
+      m_name+=".";
+      m_name+=ppfy->getName();
+    };
+
+  string getName() const {return m_name;};
+  };*/
+
+#endif