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Revision 1.3 - (view) (download) (as text)
| 1 : | hwang | 1.1 | #include <stdio.h> |
| 2 : | #include <string> | ||
| 3 : | #include <vector> | ||
| 4 : | #include <set> | ||
| 5 : | #include <iterator> | ||
| 6 : | #include <fstream> | ||
| 7 : | #include <iostream> | ||
| 8 : | #include <sys/timeb.h> | ||
| 9 : | |||
| 10 : | #include "RecoReadout/RecoElem.hh" | ||
| 11 : | #include "RecoReadout/Reaction.hh" | ||
| 12 : | #include "MExplorer/xduGen.hh" | ||
| 13 : | |||
| 14 : | #include "sbml/SBMLReader.h" | ||
| 15 : | #include "sbml/SBMLTypes.h" | ||
| 16 : | |||
| 17 : | |||
| 18 : | using namespace std; | ||
| 19 : | |||
| 20 : | //************************************************************************ | ||
| 21 : | |||
| 22 : | |||
| 23 : | RecoElem* SBMLtoRecoElem(Model_t* m); | ||
| 24 : | void inreaction(Reaction_t* r, vector<Reaction>& rxns); | ||
| 25 : | void printList (RecoElem& elem); | ||
| 26 : | //************************************************************************ | ||
| 27 : | |||
| 28 : | |||
| 29 : | |||
| 30 : | |||
| 31 : | //************************************************************************ | ||
| 32 : | int | ||
| 33 : | main(int argc, char* argv[] ) { | ||
| 34 : | //************************************************************************ | ||
| 35 : | |||
| 36 : | |||
| 37 : | SBMLDocument_t *d; | ||
| 38 : | Model_t *m; | ||
| 39 : | |||
| 40 : | if (argc != 2) | ||
| 41 : | { | ||
| 42 : | printf("usage: readSBML <filename>\n"); | ||
| 43 : | return 1; | ||
| 44 : | } | ||
| 45 : | |||
| 46 : | |||
| 47 : | d = readSBML(argv[1]); | ||
| 48 : | |||
| 49 : | m = d->model; | ||
| 50 : | if (0==m) { | ||
| 51 : | cout << "Did not read model " << argv[1] << endl; | ||
| 52 : | exit( 1 ); | ||
| 53 : | } | ||
| 54 : | |||
| 55 : | RecoElem* elem = SBMLtoRecoElem (m); | ||
| 56 : | |||
| 57 : | cout << "************************" << endl; | ||
| 58 : | printList(*elem); | ||
| 59 : | cout << "************************" << endl; | ||
| 60 : | |||
| 61 : | std::string path=""; | ||
| 62 : | xduGen( *elem, path ); | ||
| 63 : | |||
| 64 : | return 0; | ||
| 65 : | } | ||
| 66 : | |||
| 67 : | |||
| 68 : | |||
| 69 : | |||
| 70 : | //************************************************************************ | ||
| 71 : | void printList (RecoElem& elem) | ||
| 72 : | //************************************************************************ | ||
| 73 : | { | ||
| 74 : | |||
| 75 : | // I don't think there's any subelements. Model w/ one subelement, and 1 kid | ||
| 76 : | |||
| 77 : | vector<RecoElem>& subElem = elem.getSubElements(); | ||
| 78 : | vector<Reaction>& rxns = elem.getReactions(); | ||
| 79 : | |||
| 80 : | int nrxns= rxns.size (); | ||
| 81 : | int nkids= subElem.size (); | ||
| 82 : | |||
| 83 : | cout << "MY NAME: " << elem.getName() << endl; | ||
| 84 : | cout << " No. of reactions " << nrxns << endl; | ||
| 85 : | cout << " No. of kids: " << nkids << endl; | ||
| 86 : | |||
| 87 : | |||
| 88 : | for (int l=0; l< nrxns ; l++) { | ||
| 89 : | efrank | 1.2 | cout << rxns[l].asString( ) << endl; |
| 90 : | hwang | 1.1 | } |
| 91 : | |||
| 92 : | |||
| 93 : | for (int i=0; i<nkids; i++){ | ||
| 94 : | cout << "in deeper **** " << endl; | ||
| 95 : | printList(subElem[i]); | ||
| 96 : | cout << "back up *** " << endl; | ||
| 97 : | } | ||
| 98 : | |||
| 99 : | return; | ||
| 100 : | } | ||
| 101 : | |||
| 102 : | |||
| 103 : | |||
| 104 : | |||
| 105 : | |||
| 106 : | //********************************************************************** | ||
| 107 : | RecoElem* | ||
| 108 : | SBMLtoRecoElem(Model_t* m) { | ||
| 109 : | //************************************************************************ | ||
| 110 : | |||
| 111 : | string name; | ||
| 112 : | int id, numreactant, numproduct; | ||
| 113 : | |||
| 114 : | Reaction_t* r; | ||
| 115 : | Species_t* s; | ||
| 116 : | List_t* rlist = m->reaction; | ||
| 117 : | |||
| 118 : | |||
| 119 : | //not sure what to put as an id, 0 for now | ||
| 120 : | name=m->name; | ||
| 121 : | id=0; | ||
| 122 : | |||
| 123 : | efrank | 1.3 | RecoElem* elem= new RecoElem( name, id); |
| 124 : | hwang | 1.1 | |
| 125 : | vector<Reaction>& rxns = elem->getReactions(); | ||
| 126 : | |||
| 127 : | |||
| 128 : | //put in reactions | ||
| 129 : | int reactionsize= List_size(rlist); | ||
| 130 : | //cout << "number of reactions " << reactionsize << endl; | ||
| 131 : | |||
| 132 : | |||
| 133 : | |||
| 134 : | for (int j=0; j< reactionsize ; j++) | ||
| 135 : | { | ||
| 136 : | |||
| 137 : | // cout << "Reaction : " << j <<endl; | ||
| 138 : | r=Model_getReaction(m,j); | ||
| 139 : | //cout << r->name << endl; | ||
| 140 : | inreaction(r,rxns); | ||
| 141 : | |||
| 142 : | // cout << endl; | ||
| 143 : | } | ||
| 144 : | |||
| 145 : | |||
| 146 : | return elem; | ||
| 147 : | |||
| 148 : | |||
| 149 : | } | ||
| 150 : | //************************************************************************ | ||
| 151 : | void | ||
| 152 : | inreaction(Reaction_t* r, vector<Reaction>& rxns) { | ||
| 153 : | //************************************************************************ | ||
| 154 : | |||
| 155 : | int id; | ||
| 156 : | int dir; | ||
| 157 : | |||
| 158 : | int numreactant=Reaction_getNumReactants(r); | ||
| 159 : | int numproduct=Reaction_getNumProducts(r); | ||
| 160 : | SpeciesReference_t* sr, *pr; | ||
| 161 : | |||
| 162 : | //id not sure what to put here | ||
| 163 : | //direction is reversible or not. false, true | ||
| 164 : | efrank | 1.2 | |
| 165 : | Reaction::Direction reDir; | ||
| 166 : | hwang | 1.1 | id=0; |
| 167 : | dir=r->reversible; | ||
| 168 : | efrank | 1.2 | Reaction rxn( id, Reaction::forward ); |
| 169 : | if ( dir ) { | ||
| 170 : | rxn.setDirection( Reaction::both ); | ||
| 171 : | } | ||
| 172 : | hwang | 1.1 | |
| 173 : | vector<string>& reactant = rxn.getInputMetaboliteNames(); | ||
| 174 : | vector<string>& product = rxn.getOutputMetaboliteNames(); | ||
| 175 : | |||
| 176 : | vector<int>& inMetabN = rxn.getInputStoich(); | ||
| 177 : | vector<int>& outMetabN = rxn.getOutputStoich(); | ||
| 178 : | |||
| 179 : | //add reactants | ||
| 180 : | //add products | ||
| 181 : | |||
| 182 : | |||
| 183 : | |||
| 184 : | //figuring out the common denominator | ||
| 185 : | int rdem = 1; | ||
| 186 : | int pdem = 1; | ||
| 187 : | int demstoich; | ||
| 188 : | |||
| 189 : | for (int j=0; j< numreactant ; j++ ) | ||
| 190 : | { | ||
| 191 : | sr=Reaction_getReactant(r,j); | ||
| 192 : | rdem= rdem * sr->denominator; | ||
| 193 : | |||
| 194 : | } | ||
| 195 : | |||
| 196 : | |||
| 197 : | for (int m=0; m<numproduct; m++) | ||
| 198 : | { | ||
| 199 : | pr=Reaction_getProduct(r,m); | ||
| 200 : | pdem= pdem * pr->denominator; | ||
| 201 : | |||
| 202 : | } | ||
| 203 : | |||
| 204 : | |||
| 205 : | demstoich = rdem * pdem; | ||
| 206 : | // cout << "common denominator: " << demstoich; | ||
| 207 : | |||
| 208 : | for (int k=0; k < numreactant ; k++ ) | ||
| 209 : | { | ||
| 210 : | sr=Reaction_getReactant(r,k); | ||
| 211 : | // cout << "test reactant: " << sr->species << endl; | ||
| 212 : | |||
| 213 : | |||
| 214 : | reactant.push_back (sr->species); | ||
| 215 : | inMetabN.push_back( demstoich * sr->stoichiometry/sr->denominator); | ||
| 216 : | } | ||
| 217 : | |||
| 218 : | //cout << rxn.asString()[0]; | ||
| 219 : | |||
| 220 : | for (int l=0; l<numproduct; l++) | ||
| 221 : | { | ||
| 222 : | |||
| 223 : | pr=Reaction_getProduct(r,l); | ||
| 224 : | // cout << "product: " << pr->species << endl; | ||
| 225 : | |||
| 226 : | product.push_back(pr->species); | ||
| 227 : | outMetabN.push_back(demstoich * pr->stoichiometry/ pr->denominator ); | ||
| 228 : | } | ||
| 229 : | |||
| 230 : | rxns.push_back(rxn); | ||
| 231 : | |||
| 232 : | return; | ||
| 233 : | } |
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