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

[jabaws.git] / binaries / src / ViennaRNA / RNAforester / src / rnaforest.cpp

diff --git a/binaries/src/ViennaRNA/RNAforester/src/rnaforest.cpp b/binaries/src/ViennaRNA/RNAforester/src/rnaforest.cpp
new file mode 100644 (file)
index 0000000..fbf79d8
--- /dev/null
+++ b/binaries/src/ViennaRNA/RNAforester/src/rnaforest.cpp
@@ -0,0 +1,183 @@
+/*
+  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 WIN32
+#include "config.h"
+#endif
+
+#ifndef HAVE_LIBRNA
+#undef HAVE_LIBG2
+#endif
+
+#include <string.h>
+
+#include "rnaforest.h"
+#include "rnafuncs.h"
+
+#include "ppforest.t.cpp"
+
+/* ****************************************** */
+/*    Constructor and Destruktor functions    */
+/* ****************************************** */
+
+RNAForest::RNAForest(const string &baseStr, const string &viennaStr, const string &name)
+: PPForest<RNA_Alphabet>(RNAFuncs::treeSize(viennaStr)),
+  m_baseStr(baseStr),
+  m_viennaStr(viennaStr)
+{      
+  if(name.empty())
+    m_name="unknown";
+  else
+    m_name=name;
+
+  buildForest(baseStr,viennaStr);
+};
+
+/* ****************************************** */
+/*            Private functions               */
+/* ****************************************** */
+
+inline void RNAForest::makeLabel(RNA_Alphabet &a,char c)
+{
+  a=c;
+}
+
+inline void RNAForest::showLabel(ostream &s,RNA_Alphabet a) const
+{
+  s << a;
+}
+
+void RNAForest::buildForest(const string &baseStr, const string &viennaStr)
+{
+       Ulong basePairCount=0,maxDepth=0,stackPtr;
+       Uint baseStrLen,viennaStrLen,node,*nodeStack, *numChildrenStack;
+
+       assert(RNAFuncs::isRNAString(baseStr));
+
+       RNAFuncs::isViennaString(viennaStr,basePairCount,maxDepth);
+
+       baseStrLen=baseStr.length();
+       viennaStrLen=viennaStr.length();
+
+       // check if base string and vienna string have the same length
+       //  if(baseStr.length() > 0)
+       //    if(baseStr.length() != viennaStrLen)
+       //      throw RNAForestExceptionInput(RNAForestExceptionInput::Error_BaseStringAndViennaStringIncompatible);
+
+       nodeStack=new Uint[maxDepth+1];
+       numChildrenStack=new Uint[maxDepth+1];   
+       memset(nodeStack,0,sizeof(Uint)*maxDepth+1);
+       memset(numChildrenStack,0,sizeof(Uint)*maxDepth+1);
+
+       // fill PPForest structure
+       stackPtr=0;
+       node=0;
+       for(Uint i=0;i<viennaStrLen;i++)
+       {               
+               switch(viennaStr[i])
+               {
+               case '.':
+                       // set label
+                       if(baseStrLen)
+                               makeLabel(m_lb[node],baseStr[i]);
+                       else
+                               makeLabel(m_lb[node],'B');                              
+
+                       // set right brother
+                       if(node==size()-1)
+                               setRightBrotherIndex(node,0);
+                       else
+                               setRightBrotherIndex(node,node+1);
+
+                       // set num children
+                       setNumChildren(node,0);
+
+                       // increase stack values
+                       numChildrenStack[stackPtr]++;
+
+                       node++;
+                       break;
+
+               case '(':
+                       // set label
+                       makeLabel(m_lb[node],'P');
+
+                       // increase stack values
+                       numChildrenStack[stackPtr]++;
+
+                       // push 
+                       stackPtr++;
+                       nodeStack[stackPtr]=node;
+                       numChildrenStack[stackPtr]=1;
+
+                       node++;
+
+                       // set label
+                       if(baseStrLen)
+                               makeLabel(m_lb[node],baseStr[i]);
+                       else
+                               makeLabel(m_lb[node],'B');
+
+                       // set right brother
+                       setRightBrotherIndex(node,node+1);
+
+                       // set num children
+                       setNumChildren(node,0);
+
+                       node++;                         
+                       break;
+               case ')':
+                       // set label
+                       if(baseStrLen)
+                               makeLabel(m_lb[node],baseStr[i]);
+                       else
+                               makeLabel(m_lb[node],'B');  
+
+                       // set right brother
+                       setRightBrotherIndex(node,0);    
+
+                       // set num children
+                       setNumChildren(node,0);  
+
+                       // pop
+                       if(node==size()-1)
+                               setRightBrotherIndex(nodeStack[stackPtr],0);
+                       else
+                               setRightBrotherIndex(nodeStack[stackPtr],node+1);  
+
+                       setNumChildren(nodeStack[stackPtr],numChildrenStack[stackPtr]+1);
+                       stackPtr--;
+
+                       node++;
+                       break;                                                  
+               }               
+       }       
+
+       delete[] nodeStack;
+       delete[] numChildrenStack;
+       calcSumUpCSF();
+       calcRMB();
+
+       assert (m_noc[m_size-1]==0);
+}
+
+/* ****************************************** */
+/*             Public functions               */
+/* ****************************************** */
+
+#ifdef HAVE_LIBG2  // This features require the g2 library
+void RNAForest::plot2d(const string &filename_prefix, const list<pair<Uint,Uint> > &regions, const RNAFuncs::SquigglePlotOptions &sqOptions) const
+{
+  RNAFuncs::drawRNAStructure(m_baseStr,m_viennaStr,filename_prefix,m_name,regions,sqOptions);
+}
+#endif