Merge branch 'writeSBML' of git.hhu.de:bioinformatik/sybilsbml into writeSBML

R/sybilSBML.R

@@ -331,8 +331,7 @@ deformatGene<-function(idstr) {
   return(idstr)
 }
 
-exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xml",validation=TRUE){
-  #morg<-modelorg[["modelorg"]] 
+exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xml",recoverExtMet=TRUE,printNotes=TRUE,printAnnos=TRUE,validation=FALSE ){
   if(class(morg)!="modelorg"){
     stop("morg has to be of class modelorg\n")
   }
@@ -382,12 +381,14 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
   ##EXCHANGE REACTIONS##
   ex <- findExchReact(morg)
   ex_react<-NULL
-  if(!is.null(ex))
+  # if recoverExtMet== FALSE => null for ex_react
+  if( (!is.null(ex)) && (recoverExtMet) )
   {
     if(!(all(diag(S(morg)[met_pos(ex), react_pos(ex)])==-1)))
       stop("exchange reactions with Scoeff different than -1\n")
     ex_react<-as.integer(react_pos(ex))
   }
+  
   ### Build wrapper for C Function #####
   
   
@@ -415,27 +416,24 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
   
   newsubS<- NULL
 
-  
-  # TODO ATRRIBUTE NUR LESEN BEI NEUER SYBIL VERSION
-  
   if( .hasSlot(morg,"mod_attr") &&  .hasSlot(morg,"comp_attr") &&  .hasSlot(morg,"met_attr")  &&  .hasSlot(morg,"react_attr") )
     newSybil<-TRUE
   else newSybil<-FALSE
   ### Start newSybil attr
   if(newSybil)
   { 
-    if("notes" %in% colnames(mod_attr(morg))) mod_notes<-as.character(mod_attr(morg)[['notes']])
-    if("annotation" %in% colnames(mod_attr(morg))) mod_annotation<-as.character(mod_attr(morg)[['annotation']])
+    if(("notes" %in% colnames(mod_attr(morg))) && (printNotes) ) mod_notes<-as.character(mod_attr(morg)[['notes']])
+    if(("annotation" %in% colnames(mod_attr(morg))) && (printAnnos) ) mod_annotation<-as.character(mod_attr(morg)[['annotation']])
     
-    if("notes" %in% colnames(comp_attr(morg))) com_notes<-as.character(as.list((comp_attr(morg)[['notes']])))
-    if("annotation" %in% colnames(comp_attr(morg))) com_annotation<-as.character(as.list((comp_attr(morg)[['annotation']])))
+    if(("notes" %in% colnames(comp_attr(morg)))    && (printNotes) ) com_notes<-as.character(as.list((comp_attr(morg)[['notes']])))
+    if(("annotation" %in% colnames(comp_attr(morg))) && (printAnnos)  ) com_annotation<-as.character(as.list((comp_attr(morg)[['annotation']])))
     
     if("charge" %in% colnames(met_attr(morg))) met_charge<- as.integer(as.list((met_attr(morg)[['charge']])))
     if("chemicalFormula" %in% colnames(met_attr(morg))) met_formula<-as.character(as.list((met_attr(morg)[['chemicalFormula']])))
-    if("annotation" %in% colnames(met_attr(morg))) met_anno<-as.character(as.list((met_attr(morg)[['annotation']])))
+    if(("annotation" %in% colnames(met_attr(morg))) && (printAnnos)) met_anno<-as.character(as.list((met_attr(morg)[['annotation']])))
     if("boundaryCondition" %in% colnames(met_attr(morg))) met_bnd<-as.logical(as.list((met_attr(morg)[['boundaryCondition']])))
     
-    if("notes" %in% colnames(met_attr(morg)))
+    if(("notes" %in% colnames(met_attr(morg))) && (printNotes) )
     {   # delete Formular and charge from notes to do
       met_notes<-as.character(as.list((met_attr(morg)[['notes']])))
       if (!is.null(met_charge) || !is.null(met_formula))
@@ -481,10 +479,10 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
       }
       
     }
-    if("annotation" %in% colnames(react_attr(morg))) react_anno<-as.character(as.list((react_attr(morg)[['annotation']])))
+    if(("annotation" %in% colnames(react_attr(morg))) && (printAnnos)) react_anno<-as.character(as.list((react_attr(morg)[['annotation']])))
     
     # Merge Notes with "our" Notes and make sure gpr Rules from gpr
-    if("notes" %in% colnames(react_attr(morg)))
+    if(("notes" %in% colnames(react_attr(morg))) && (printNotes))
     {
       react_notes<-as.character(as.list((react_attr(morg)[['notes']])))
       # using
@@ -565,6 +563,7 @@ exportSBML<- function(morg=NULL,level=2,version=4,FbcLevel=0,filename="export.xm
                   react_notes,
                   react_anno,
                   ex_react,
+                  as.logical(validation),
                   as.character(deformatGene(allgenes))
   )
   return (success)

src/init.c

@@ -54,7 +54,7 @@ static const R_CallMethodDef callMethods[] = {
     {"getSBMLCompartList",         (DL_FUNC) &getSBMLCompartList,         1},
     {"getSBMLSpeciesList",         (DL_FUNC) &getSBMLSpeciesList,         1},
     {"getSBMLReactionsList",       (DL_FUNC) &getSBMLReactionsList,       1},
-    {"exportSBML",                 (DL_FUNC) &exportSBML,                 33},
+    {"exportSBML",                 (DL_FUNC) &exportSBML,                 34},
     {"getSBMLFbcversion",          (DL_FUNC) &getSBMLFbcversion,          1},
     {NULL, NULL, 0}
 };

src/sybilSBML.c

@@ -1605,7 +1605,7 @@ void ParseModtoAnno  (SBase_t* comp , char* Mannocopy)
 
 
 
-SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react, SEXP allgenes)
+SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react,SEXP validation, SEXP allgenes)
 {
   //Varaibles from R
   const char* fname = CHAR(STRING_ELT(filename, 0));
@@ -1791,7 +1791,6 @@ SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybi
     Compartment_setId(comp,sName);
     Compartment_setConstant(comp,1);
     if( strcmp(sName,"BOUNDARY")==0 || strcmp(sName,"Boundary")==0  || strcmp(sName,"boundary")==0)hasBoundary=1;
-    
     if (!Rf_isNull(com_notes) && Rf_length(com_notes) > 1) 
     {  
       char *Cnotes = (char*) CHAR(STRING_ELT(com_notes, i));
@@ -1819,7 +1818,7 @@ SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybi
   
   
   /* Boundary Compartment */
-  if(hasBoundary==0 && Rf_isNull(met_bnd) && Rf_length(met_bnd) <= 1 )
+  if(hasBoundary==0 && Rf_isNull(met_bnd) && Rf_length(met_bnd) <= 1 && !Rf_isNull(ex_react))
   {  
   comp = Model_createCompartment(model);
   Compartment_setId(comp,"BOUNDARY");
@@ -1903,13 +1902,8 @@ SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybi
       
       if((Manno != NULL) && (Manno[0] != '\0' )) 
       {  
-        //XMLNode_t * xmlannotation= RDFAnnotationParser_createAnnotation();
-        //XMLNode_t *rdf=RDFAnnotationParser_createRDFAnnotation(2,4);
-        //XMLNode_addChild(xmlannotation,(const XMLNode_t*) rdf);
 
-        //char *Mmetaid = (char*) CHAR(STRING_ELT(met_metaid, i));
         SBase_setMetaId((SBase_t*)sp, CHAR(STRING_ELT(met_id, i)));
-        //SBase_appendAnnotation((SBase_t*)sp, xmlannotation ); 
         
         // COPY STRING  
         char *Manno   = (char*) CHAR(STRING_ELT(met_anno, i));
@@ -2094,7 +2088,7 @@ SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybi
             SpeciesReference_setStoichiometry(spr, fabs(REAL(SMatrix)[hash]));
             
             //is Exchange Reaction
-            if(isexchange==1)
+            if(isexchange==1 && !Rf_isNull(ex_react))
             {
               /* Create boundary Species */
               sp = Model_createSpecies(model);
@@ -2281,6 +2275,20 @@ SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybi
     }  
   }
   
+  // if VALIDATION TRUE FIND ERRORS
+  if(LOGICAL(validation)[0]==1)
+  {
+    unsigned int       errors = 0;
+    errors  = SBMLDocument_getNumErrors(sbmlDoc);
+   // errors += SBMLDocument_checkConsistency(sbmlDoc); warnings
+    if (errors > 0){
+    SBMLDocument_printErrors(sbmlDoc, stdout);
+    printf("\n");
+    }
+    else printf("No errors \n");
+  }  
+
+  // write SBML file
   int result = writeSBML(sbmlDoc, fname);
   SEXP out = R_NilValue;
   if (result) out = Rf_mkString(append_strings("Wrote file",fname," "));

src/sybilSBML.h

@@ -109,5 +109,5 @@ SEXP getSBMLSpeciesList(SEXP sbmlmod);
 SEXP getSBMLReactionsList(SEXP sbmlmod);
 
 /* export Modelorg to SBML*/
-SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react, SEXP allgenes);
+SEXP exportSBML (SEXP version, SEXP level,SEXP FbcLevel, SEXP filename,SEXP sybil_max, SEXP mod_desc, SEXP mod_name, SEXP mod_compart, SEXP met_id, SEXP met_name, SEXP met_comp, SEXP met_form,SEXP met_charge, SEXP react_id, SEXP react_name, SEXP react_rev, SEXP lowbnd, SEXP uppbnd, SEXP obj_coef, SEXP subSys, SEXP gpr, SEXP SMatrix, SEXP mod_notes, SEXP mod_anno, SEXP com_notes , SEXP com_anno, SEXP met_notes, SEXP met_anno, SEXP met_bnd , SEXP react_notes, SEXP react_anno, SEXP ex_react,SEXP validation, SEXP allgenes);