Added utility functions to initialize and hold a struct for passing around the RNA info to functions for increased maintainability

dfsdsdf

@@ -0,0 +1,30 @@
+  origin/556-optim-update-sequence-range-visibility
+  origin/EdPknotFixBug
+  origin/EternaJS-new-oligo-method
+  origin/HEAD -> origin/dev
+  origin/OligoEnergyBug
+  origin/batch-renderer
+  origin/codon-cycler
+  origin/complexesAndConcentrations
+  origin/cypress
+  origin/degscore_predict
+  origin/dependabot/npm_and_yarn/three-0.125.0
+  origin/dev
+  origin/duplicate-buttons-for-drag-and-drop
+  origin/ensembleDefect
+  origin/eterna-nova
+  origin/eterna2-skeleton
+  origin/fix-zoom-centering
+  origin/i18n-tempaltetag
+  origin/master
+  origin/mercedconfig
+  origin/new-state-managment
+  origin/new-toolbar-updates
+  origin/offline
+  origin/pr-new_toolbar
+  origin/puzzlemaker-constraints
+  origin/scripts-changes
+  origin/sheila
+  origin/studs
+  origin/trunk
+  origin/v2

lib/NUPACK/emscripten/FullEnsemble.cpp

@@ -21,74 +21,33 @@ extern int Multistranded;
 FullAdvancedResult* FullEnsembleWithOligos(const std::string& seqString, int temperature, float kcalDeltaRange, bool const pseudoknotted = false) {
 
     //this chuck of code sets up the variables used to represent adn configure the sequence for the C code to use
-    auto autoSeqString = MakeCString(seqString);
-    char* string = autoSeqString.get();
-    int seqNum[MAXSEQLENGTH+1];
-
-
-
-    //runtime_constants.h defines NAD_INFINITY
-    //#define NAD_INFINITY 100000 //artificial value for positive infinity
-    //this is how teh dnastructure call looks for subopt.c which is waht iran when you ron normal nupack compiled code
-    //here are comments from pfuncutilheaders.h on hwat the attributes of dnastructures consist of
-
-    //oneDnaStruct and dnaStructures are used for enumerating sequences
-       // typedef struct {
-       // int *theStruct; //describes what is paired to what
-       // DBL_TYPE error; //accumulated error (from the mfe) for a structure
-       // DBL_TYPE correctedEnergy; //actual energy of a structure
-       // int slength;
-       // //(accounting for symmetry).
-       //  } oneDnaStruct;
-       //
-       // typedef struct {
-       // oneDnaStruct *validStructs;
-       //int nStructs; //# of structures stored
-       //int nAlloc; //# of structures allocated
-       // int seqlength;
-       // DBL_TYPE minError; //minimum deviation from mfe for all seqs
-       //in validStructs
-       //
-       //} dnaStructures;
-
-    //this struct will store
-    //all the structures within the given range
-    dnaStructures suboptStructs = {NULL, 0, 0, 0, NAD_INFINITY}; 
-
-    //convert from how it comes from eterna to how nuapck needs it for joined oligos '+'
-    char* pc;
-    do {
-        pc = strchr(string, '&');
-        if (pc) (*pc) = '+';
-    } while(pc);
+    SequenceStructureInfo rna_info = SequenceStructureInfo();
+    setSequenceInfo(seqString, &rna_info);
 
-
-    int seqStringLength = strlen(string);    
-    convertSeq(string, seqNum, seqStringLength);
-
-
     //first get the ensemble through subopt
-    if ( pseudoknotted ) {
-        mfeFullWithSym_SubOpt(seqNum, seqStringLength, &suboptStructs, 5, RNA, 1 /*DANGLETYPE*/, 
-                                temperature, TRUE, (DBL_TYPE) kcalDeltaRange, 
+    if ( rna_info.isPknot==TRUE ) {
+        mfeFullWithSym_SubOpt(rna_info.sequenceNumber, rna_info.sequenceLength, &rna_info.ensemebleStructs, 5, RNA, 1 /*DANGLETYPE*/, 
+                                rna_info.temperature, TRUE, (DBL_TYPE) kcalDeltaRange, 
                                 0, SODIUM_CONC, MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
     } else {
-        mfeFullWithSym_SubOpt(seqNum, seqStringLength, &suboptStructs, 3, RNA, 1 /*DANGLETYPE*/, 
-                                temperature, TRUE, (DBL_TYPE) kcalDeltaRange, 
+        mfeFullWithSym_SubOpt(rna_info.sequenceNumber, rna_info.sequenceLength, &rna_info.ensemebleStructs, 3, RNA, 1 /*DANGLETYPE*/, 
+                                rna_info.temperature, TRUE, (DBL_TYPE) kcalDeltaRange, 
                                 0, SODIUM_CONC, MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
     }
 
+
+    //now process the results for return to TS
     //initialize the result to return
     FullAdvancedResult* result = new FullAdvancedResult();
 
     int i, j;
     //get dot bracket notation from data 
-    for (i = 0; i < suboptStructs.nStructs; i++ ) {
-        oneDnaStruct currentStruct = suboptStructs.validStructs[i];
+    for (i = 0; i < rna_info.ensemebleStructs.nStructs; i++ ) {
+        oneDnaStruct currentStruct = rna_info.ensemebleStructs.validStructs[i];
 
         //each structure reset this
         std::string singlestructure = "";             
-        for (j = 0; j < suboptStructs.seqlength; j++ ) {
+        for (j = 0; j < rna_info.ensemebleStructs.seqlength; j++ ) {
             if ( currentStruct.theStruct[j] > j ) {
                 singlestructure.push_back('(');
             }
@@ -98,9 +57,9 @@ FullAdvancedResult* FullEnsembleWithOligos(const std::string& seqString, int tem
             else singlestructure.push_back(')');
         }  
 
-
+        char* pc;
         std::string constraints = singlestructure;
-        for (pc = string, i = 0, j = 0; (*pc); pc++, j++) {
+        for (pc = rna_info.sequenceChar, i = 0, j = 0; (*pc); pc++, j++) {
             auto value = ((*pc) == '+' ? '&' : constraints[i++]);
             if (j < singlestructure.length()) {
                 singlestructure[j] = value;
@@ -120,176 +79,106 @@ FullAdvancedResult* FullEnsembleWithOligos(const std::string& seqString, int tem
         result->suboptFreeEnergy.push_back(correctedEnergy);
     }
 
-    clearDnaStructures(&suboptStructs);
+
+    clearDnaStructures(&rna_info.ensemebleStructs);
+
     return result;
 }
 
 
 FullAdvancedResult* FullEnsembleNoBindingSite(const std::string& seqString, int temperature, float kcalDeltaRange, bool const pseudoknotted = false) {
 
-    //this chuck of code sets up the variables used to represent adn configure the sequence for the C code to use
-    auto autoSeqString = MakeCString(seqString);
-    char* string = autoSeqString.get();
-    int seqNum[MAXSEQLENGTH+1];
-    int seqStringLength = strlen(string);
-    //runtime_constants.h defines NAD_INFINITY
-    //#define NAD_INFINITY 100000 //artificial value for positive infinity
-    //this is how teh dnastructure call looks for subopt.c which is waht iran when you ron normal nupack compiled code
-    //here are comments from pfuncutilheaders.h on hwat the attributes of dnastructures consist of
-
-    //oneDnaStruct and dnaStructures are used for enumerating sequences
-       // typedef struct {
-       // int *theStruct; //describes what is paired to what
-       // DBL_TYPE error; //accumulated error (from the mfe) for a structure
-       // DBL_TYPE correctedEnergy; //actual energy of a structure
-       // int slength;
-       // //(accounting for symmetry).
-       //  } oneDnaStruct;
-       //
-       // typedef struct {
-       // oneDnaStruct *validStructs;
-       //int nStructs; //# of structures stored
-       //int nAlloc; //# of structures allocated
-       // int seqlength;
-       // DBL_TYPE minError; //minimum deviation from mfe for all seqs
-       //in validStructs
-       //
-       //} dnaStructures;
-
-    //this struct will store
-    //all the structures within the given range
-    dnaStructures suboptStructs = {NULL, 0, 0, 0, NAD_INFINITY};     
-    convertSeq(string, seqNum, seqStringLength);
-
-
-
+    SequenceStructureInfo rna_info = SequenceStructureInfo();
+    setSequenceInfo(seqString, &rna_info);   
+    setGlobals(NULL, NULL, pseudoknotted, temperature, &rna_info);      
+
     //first get the ensemble through subopt
-    if ( pseudoknotted ) {
-        mfeFullWithSym_SubOpt(seqNum, seqStringLength, &suboptStructs, 5, RNA, 1 /*DANGLETYPE*/, 
-                                temperature, TRUE, (DBL_TYPE) kcalDeltaRange, 
+    if ( rna_info.isPknot == TRUE ) {
+        mfeFullWithSym_SubOpt(rna_info.sequenceNumber, rna_info.sequenceLength, &rna_info.ensemebleStructs, 5, RNA, 1 /*DANGLETYPE*/, 
+                                rna_info.temperature, TRUE, (DBL_TYPE) kcalDeltaRange, 
                                 0, SODIUM_CONC, MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
     } else {
-        mfeFullWithSym_SubOpt(seqNum, seqStringLength, &suboptStructs, 3, RNA, 1 /*DANGLETYPE*/, 
-                                temperature, TRUE, (DBL_TYPE) kcalDeltaRange, 
+        mfeFullWithSym_SubOpt(rna_info.sequenceNumber, rna_info.sequenceLength, &rna_info.ensemebleStructs, 3, RNA, 1 /*DANGLETYPE*/, 
+                                rna_info.temperature, TRUE, (DBL_TYPE) kcalDeltaRange, 
                                 0, SODIUM_CONC, MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
     }
 
-    //initialize the result to return
-
+
+    //now process the results for return to TS
+    //initialize the result to return    
+
     FullAdvancedResult* result = new FullAdvancedResult();
 
     std::string mfeStructure;
     //get dot bracket notation from data 
-    for ( int i = 0; i < suboptStructs.nStructs; i++ ) {
-        oneDnaStruct currentStruct = suboptStructs.validStructs[i];
+
+    for ( int i = 0; i < rna_info.ensemebleStructs.nStructs; i++ ) {
+        rna_info.currentStruct = rna_info.ensemebleStructs.validStructs[i];
 
         //get the secondary strucutre in dot paren notation 
-        std::string singlestructure = getDotParens(pseudoknotted, suboptStructs.seqlength, &currentStruct);
+        std::string singlestructure = getDotParens(pseudoknotted, rna_info.ensemebleStructs.seqlength, &rna_info.currentStruct);
+
         if (i == 0)
         {
           //this is the first one so it is the mfe          
           mfeStructure = singlestructure;
         }
 
         //get energies
-        double energyError = currentStruct.error;
-        double correctedEnergy = currentStruct.correctedEnergy;  
+        double energyError = rna_info.currentStruct.error;
+        double correctedEnergy = rna_info.currentStruct.correctedEnergy;  
 
-
+        //std::string test(rna_info.sequenceNumber);
+        std::string test;
+        for (int j =0; j < rna_info.sequenceLength; j++) {
+               test = test + std::to_string(rna_info.sequenceNumber[j]); 
+        }
         //write out data
         result->suboptStructures.push_back(singlestructure);
         result->suboptEnergyError.push_back(energyError);
         result->suboptFreeEnergy.push_back(correctedEnergy);
     }
 
-    clearDnaStructures(&suboptStructs);
+
+    clearDnaStructures(&rna_info.ensemebleStructs);
+
 
     return result;
 }
 
-/*
-  mode is how to do the ED
-  1= do only ED
-  2 = do only MFE ED
-  3 = do both
-*/
+
 
 FullEnsembleDefectResult* GetEnsembleDefect(const std::string& seqString, const std::string& MfeStructure, int temperature, bool pseudoknot) {
 
-  FullEnsembleDefectResult* result = new FullEnsembleDefectResult();  
-  int complexity;
-  DBL_TYPE nsStar_ED;
-  int i;
-  int nNicks;
-  int seqlength;
-  int tmpLength;
-  int seqNum[MAXSEQLENGTH+1];
-
-  //set the globals 
-  USE_MFE=0;
-  ONLY_ONE_MFE=0;   
-
-  if (pseudoknot == true) {
-      DO_PSEUDOKNOTS = 1;
-  } else {
-      DO_PSEUDOKNOTS = 0;
-  }
-
-  if ( !DO_PSEUDOKNOTS ) {
-      complexity = 3;
-  } else {
-      complexity = 5;
-  }
-
-
-  //convert sequence from string to char*
-  auto autoSeqString = MakeCString(seqString);
-  char* seqChar = autoSeqString.get();
-
+    FullEnsembleDefectResult* result = new FullEnsembleDefectResult(); 
+
+    SequenceStructureInfo rna_info = SequenceStructureInfo();
+    setSequenceInfo(seqString, &rna_info);
+    setStructureInfo(MfeStructure, &rna_info);
+    setGlobals(FALSE,FALSE,pseudoknot,temperature, &rna_info);
 
-  //convert sequence from latin based characters "A,C,U,G" into numerical representation A=1, C=2, G=3. U=4 
-  seqlength = tmpLength = strlen(seqChar);
-  convertSeq(seqChar, seqNum, tmpLength);
-
-  // Get the number of strand breaks
-  nNicks = 0;
-  for (i = 0; i < tmpLength; i++) {
-      if (seqChar[i] == '+') {
-          nNicks++;
-      }
-  }
-
-  // New sequence length removing the number of breaks or pluses from the total
-  seqlength -= nNicks;
+    DBL_TYPE nsStar_ED;
+
+    // Allocate memory for storing pair probabilities
+    pairPr = (DBL_TYPE*) calloc( (rna_info.sequenceLength+1)*(rna_info.sequenceLength+1), sizeof(DBL_TYPE));
+    // Allocate memory for storing pair probabilities
+    pairPrPbg = (DBL_TYPE*) calloc( (rna_info.sequenceLength+1)*(rna_info.sequenceLength+1), sizeof(DBL_TYPE));
+    pairPrPb = (DBL_TYPE*) calloc( (rna_info.sequenceLength+1)*(rna_info.sequenceLength+1), sizeof(DBL_TYPE));
 
-  //convert the string structure to a char array
-  auto autoMfeStructure = MakeCString(MfeStructure);
-  char* MfeStructureChar = autoMfeStructure.get();
 
-  //get the pairs from the struct
-  int thepairs[MAXSEQLENGTH+1];
-  getStructureFromParens(MfeStructureChar, thepairs, seqlength);  
-
-  // Allocate memory for storing pair probabilities
-  pairPr = (DBL_TYPE*) calloc( (seqlength+1)*(seqlength+1), sizeof(DBL_TYPE));
-  // Allocate memory for storing pair probabilities
-  pairPrPbg = (DBL_TYPE*) calloc( (seqlength+1)*(seqlength+1), sizeof(DBL_TYPE));
-  pairPrPb = (DBL_TYPE*) calloc( (seqlength+1)*(seqlength+1), sizeof(DBL_TYPE));
+    nsStar_ED = nsStarPairsOrParensFull(rna_info.sequenceLength, rna_info.sequenceNumber, rna_info.thePairs, NULL,
+                rna_info.complexity, RNA, 1 /*DANGLETYPE*/,
+                rna_info.temperature, SODIUM_CONC,
+                MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
 
+
+    result->ensembleDefect = (long double) nsStar_ED;
+    result->ensembleDefectNormalized = (long double) nsStar_ED/rna_info.sequenceLength;
 
-  nsStar_ED = nsStarPairsOrParensFull(seqlength, seqNum, thepairs, NULL,
-            complexity, RNA, 1 /*DANGLETYPE*/,
-            temperature, SODIUM_CONC,
-            MAGNESIUM_CONC, USE_LONG_HELIX_FOR_SALT_CORRECTION);
+    free(pairPrPbg);
+    free(pairPrPb);
 
-
-  result->ensembleDefect = (long double) nsStar_ED;
-  result->ensembleDefectNormalized = (long double) nsStar_ED/seqlength;
-
-  free(pairPr);
-  free(pairPrPbg);
-  free(pairPrPb);
+    return result;
 
-  return result;
 }
 

lib/NUPACK/emscripten/FullEnsemble.h

@@ -13,7 +13,9 @@ struct FullAdvancedResult {
 
 struct FullEnsembleDefectResult {
     double ensembleDefect;    
-    double ensembleDefectNormalized;    
+
+    double ensembleDefectNormalized;
+
 };
 
 FullAdvancedResult* FullEnsembleNoBindingSite (const std::string& seqString, int temperature, float kcalDeltaRange, bool const pseudoknotted);