Changeset 737 for library/bdm/base

Timestamp:

11/25/09 12:14:38 (15 years ago)

Author:

mido

Message:

ASTYLER RUN OVER THE WHOLE LIBRARY, JUPEE

Location:

library/bdm/base

Files:

• bdmbase.cpp (modified) (5 diffs)
• bdmbase.h (modified) (32 diffs)
• datasources.cpp (modified) (5 diffs)
• datasources.h (modified) (7 diffs)
• loggers.cpp (modified) (2 diffs)
• loggers.h (modified) (3 diffs)
• user_info.cpp (modified) (4 diffs)
• user_info.h (modified) (12 diffs)

library/bdm/base/bdmbase.cpp

@@ -19 +19 @@
 }
 
-string RV::show_all(){
-  ostringstream os;
-  for(str2int_map::const_iterator iter=MAP.begin(); iter!=MAP.end(); iter++){
-          os << "key: " << iter->first << " val: " << iter->second <<endl;
-  }
-  return os.str();
+string RV::show_all() {
+        ostringstream os;
+        for ( str2int_map::const_iterator iter = MAP.begin(); iter != MAP.end(); iter++ ) {
+                os << "key: " << iter->first << " val: " << iter->second << endl;
+        }
+        return os.str();
 };
 
@@ -31 +31 @@
         int id;
         str2int_map::const_iterator iter = MAP.find ( name );
-        if ( iter == MAP.end() || name.length()==0) { //add new RV
+        if ( iter == MAP.end() || name.length() == 0 ) { //add new RV
                 id = MAP.size() + 1;
                 //debug
@@ -49 +49 @@
                 NAMES ( id ) = name;
                 SIZES ( id ) = size;
-                bdm_assert(size>0, "RV "+ name +" does not exists. Default size (-1) can not be assigned ");
+                bdm_assert ( size > 0, "RV " + name + " does not exists. Default size (-1) can not be assigned " );
         } else {
                 id = iter->second;
-                if (size>0 && name.length()>0){
-                        bdm_assert ( SIZES ( id ) == size, "RV " + name + " of size " + num2str(SIZES(id)) + " exists, requested size " + num2str(size) + "can not be assigned" );
+                if ( size > 0 && name.length() > 0 ) {
+                        bdm_assert ( SIZES ( id ) == size, "RV " + name + " of size " + num2str ( SIZES ( id ) ) + " exists, requested size " + num2str ( size ) + "can not be assigned" );
                 }
         }
@@ -368 +368 @@
 
 void RV::to_setting ( Setting &set ) const {
-        Array<string> names(len);
-        ivec sizes(len);
-        for (int i=0; i<len;i++){names(i)=name(i);sizes(i)=size(i);}
-        UI::save(names,set,"names");
-        UI::save(sizes,set,"sizes");
-        UI::save(times,set,"times");
+        Array<string> names ( len );
+        ivec sizes ( len );
+        for ( int i = 0; i < len; i++ ) {
+                names ( i ) = name ( i );
+                sizes ( i ) = size ( i );
+        }
+        UI::save ( names, set, "names" );
+        UI::save ( sizes, set, "sizes" );
+        UI::save ( times, set, "times" );
 }
 
@@ -402 +405 @@
 void BM::bayes_batch ( const mat &Data, const mat &Cond ) {
         for ( int t = 0; t < Data.cols(); t++ ) {
-                bayes ( Data.get_col ( t ), Cond.get_col(t) );
-        }
-}
-}
+                bayes ( Data.get_col ( t ), Cond.get_col ( t ) );
+        }
+}
+}

library/bdm/base/bdmbase.h

@@ -149 +149 @@
         friend std::ostream &operator<< ( std::ostream &os, const RV &rv );
 
-        string to_string() const {ostringstream o; o << *this; return o.str();}
-        
+        string to_string() const {
+                ostringstream o;
+                o << *this;
+                return o.str();
+        }
+
         //! total size of a random variable
         int _dsize() const {
@@ -183 +187 @@
         //! returns name of a scalar at position scalat, i.e. it can be in the middle of vector name, in that case it adds "_%d" to it
         std::string scalarname ( int scalat ) const {
-                bdm_assert(scalat<dsize,"Wrong input index");
-                int id=0;
-                int scalid=0;
-                while (scalid+SIZES(ids(id))<=scalat)  { scalid+=SIZES(ids(id)); id++;};
+                bdm_assert ( scalat < dsize, "Wrong input index" );
+                int id = 0;
+                int scalid = 0;
+                while ( scalid + SIZES ( ids ( id ) ) <= scalat )  {
+                        scalid += SIZES ( ids ( id ) );
+                        id++;
+                };
                 //now id is the id of variable of interest
-                if (size(id)==1)
+                if ( size ( id ) == 1 )
                         return  NAMES ( ids ( id ) );
                 else
-                        return  NAMES ( ids ( id ) )+ "_" + num2str(scalat-scalid);
+                        return  NAMES ( ids ( id ) ) + "_" + num2str ( scalat - scalid );
 
         }
@@ -233 +240 @@
         }
         //! create new RV from the current one with time shifted by given value
-        RV copy_t(int dt) const {
-                RV tmp=*this;
-                tmp.t_plus(dt);
+        RV copy_t ( int dt ) const {
+                RV tmp = *this;
+                tmp.t_plus ( dt );
                 return tmp;
         }
@@ -266 +273 @@
         //! Minimum time-offset
         int mint() const {
-                return times.length()>0 ? min (times) : 0;
+                return times.length() > 0 ? min ( times ) : 0;
         }
         //! Minimum time-offset of ids of given RVs
-        int mint(const RV &rv) const {
-                bvec belong=zeros_b(len);
-                for (int r=0; r<rv.length(); r++){
-                        belong = belong | (ids == rv.id(r));
-                }
-                return times.length()>0 ? min (get_from_bvec(times,belong)) : 0;
+        int mint ( const RV &rv ) const {
+                bvec belong = zeros_b ( len );
+                for ( int r = 0; r < rv.length(); r++ ) {
+                        belong = belong | ( ids == rv.id ( r ) );
+                }
+                return times.length() > 0 ? min ( get_from_bvec ( times, belong ) ) : 0;
         }
         //!@}
@@ -281 +288 @@
 
         \code
-        class = 'RV';                   
+        class = 'RV';
         names = {'a', 'b', 'c', ...};   // UNIQUE IDENTIFIER same names = same variable
-                                                                        // names are also used when storing results 
+                                                                        // names are also used when storing results
         --- optional ---
         sizes = [1, 2, 3, ...];         // size of each name. default = ones()
@@ -292 +299 @@
         void from_setting ( const Setting &set );
 
-        void to_setting( Setting &set ) const;
+        void to_setting ( Setting &set ) const;
 
         //! Invalidate all named RVs. Use before initializing any RV instances, with care...
@@ -312 +319 @@
 */
 class logger : public root {
-        protected:
-                //! RVs of all logged variables.
-                Array<RV> entries;
-                //! Names of logged quantities, e.g. names of algorithm variants
-                Array<string> names;
-                //!separator of prefixes of entries
-                const string separator;
-                //! Root Setting for storing Settings
-                Config setting_conf;
-                //! list of Settings for specific ids
-                Array<Setting*> settings;
-        public:
-                //!Default constructor
-                logger(const string separator0) : entries ( 0 ), names ( 0 ), separator(separator0) {}
-                
-                //! returns an identifier which will be later needed for calling the \c logit() function
-                //! For empty RV it returns -1, this entry will be ignored by \c logit().
-                virtual int add_vector ( const RV &rv, string prefix = "" ) {
-                        int id;
-                        if ( rv._dsize() > 0 ) {
-                                id = entries.length();
-                                names = concat ( names, prefix ); // diff
-                                entries.set_length ( id + 1, true );
-                                entries ( id ) = rv;
-                        } else {
-                                id = -1;
-                        }
-                        return id; // identifier of the last entry
-                }
-                virtual int add_setting(const string &prefix){
-                        Setting &root=setting_conf.getRoot();
-                        int id=root.getLength(); //root must be group!!
-                        if (prefix.length()>0){
-                                settings.set_length(id+1,true);
-                                settings(id) = &root.add(prefix, Setting::TypeList);
-                        } else {id=-1;}
-                        return id;
-                }
-                
-                //! log this vector
-                virtual void log_vector ( int id, const vec &v ) {
-                        bdm_error ( "Not implemented" );
-                };
-                
-                virtual Setting & log_to_setting (int id){
-                        return settings(id)->add(Setting::TypeGroup);
-                }
-                
-                //! log this double
-                virtual void logit ( int id, const double &d ) {
-                        bdm_error ( "Not implemented" );
-                };
-                
-                //! Shifts storage position for another time step.
-                virtual void step() {
-                        bdm_error ( "Not implemneted" );
-                };
-                
-                //! Finalize storing information
-                virtual void finalize() {};
-                
-                //! Initialize the storage
-                virtual void init() {};
-                
-                //!separator of prefixes for this logger
-                const string& prefix_sep() {return separator;}
+protected:
+        //! RVs of all logged variables.
+        Array<RV> entries;
+        //! Names of logged quantities, e.g. names of algorithm variants
+        Array<string> names;
+        //!separator of prefixes of entries
+        const string separator;
+        //! Root Setting for storing Settings
+        Config setting_conf;
+        //! list of Settings for specific ids
+        Array<Setting*> settings;
+public:
+        //!Default constructor
+        logger ( const string separator0 ) : entries ( 0 ), names ( 0 ), separator ( separator0 ) {}
+
+        //! returns an identifier which will be later needed for calling the \c logit() function
+        //! For empty RV it returns -1, this entry will be ignored by \c logit().
+        virtual int add_vector ( const RV &rv, string prefix = "" ) {
+                int id;
+                if ( rv._dsize() > 0 ) {
+                        id = entries.length();
+                        names = concat ( names, prefix ); // diff
+                        entries.set_length ( id + 1, true );
+                        entries ( id ) = rv;
+                } else {
+                        id = -1;
+                }
+                return id; // identifier of the last entry
+        }
+        virtual int add_setting ( const string &prefix ) {
+                Setting &root = setting_conf.getRoot();
+                int id = root.getLength(); //root must be group!!
+                if ( prefix.length() > 0 ) {
+                        settings.set_length ( id + 1, true );
+                        settings ( id ) = &root.add ( prefix, Setting::TypeList );
+                } else {
+                        id = -1;
+                }
+                return id;
+        }
+
+        //! log this vector
+        virtual void log_vector ( int id, const vec &v ) {
+                bdm_error ( "Not implemented" );
+        };
+
+        virtual Setting & log_to_setting ( int id ) {
+                return settings ( id )->add ( Setting::TypeGroup );
+        }
+
+        //! log this double
+        virtual void logit ( int id, const double &d ) {
+                bdm_error ( "Not implemented" );
+        };
+
+        //! Shifts storage position for another time step.
+        virtual void step() {
+                bdm_error ( "Not implemneted" );
+        };
+
+        //! Finalize storing information
+        virtual void finalize() {};
+
+        //! Initialize the storage
+        virtual void init() {};
+
+        //!separator of prefixes for this logger
+        const string& prefix_sep() {
+                return separator;
+        }
 };
 
@@ -429 +440 @@
         //! @{
 
-        pdf() : dimc ( 0 ), rvc(), dim(0), rv() { }
-
-        pdf ( const pdf &m ) : dimc ( m.dimc ), rvc ( m.rvc ), dim( m.dim), rv( m.rv ) { }
-        
+        pdf() : dimc ( 0 ), rvc(), dim ( 0 ), rv() { }
+
+        pdf ( const pdf &m ) : dimc ( m.dimc ), rvc ( m.rvc ), dim ( m.dim ), rv ( m.rv ) { }
+
         //! copy of the current object - make sure to implement
-        virtual pdf* _copy_() const {return new pdf(*this);}
+        virtual pdf* _copy_() const {
+                return new pdf ( *this );
+        }
         //!@}
 
@@ -488 +501 @@
 
         //! access function
-        void set_dim(int d) {dim=d;}
+        void set_dim ( int d ) {
+                dim = d;
+        }
         //! access function
-        void set_dimc(int d) {dimc=d;}
+        void set_dimc ( int d ) {
+                dimc = d;
+        }
         //! Load from structure with elements:
         //!  \code
@@ -535 +552 @@
         @{*/
         epdf() {};
-        epdf ( const epdf &e ) : pdf(e) {};
+        epdf ( const epdf &e ) : pdf ( e ) {};
         void set_parameters ( int dim0 ) {
                 dim = dim0;
         }
-        epdf* _copy_() const {return new epdf(*this);}
+        epdf* _copy_() const {
+                return new epdf ( *this );
+        }
         //!@}
 
@@ -603 +622 @@
         //!  #1 mean
         //!  #2 mean + lower & upper bound
-        void log_register(logger &L, const string &prefix){
+        void log_register ( logger &L, const string &prefix ) {
                 RV r;
                 if ( isnamed() ) {
@@ -610 +629 @@
                         r = RV ( "", dimension() );
                 };
-                root::log_register(L,prefix);
-                
+                root::log_register ( L, prefix );
+
                 // log full data
-                if (log_level==10) {
-                        logrec->ids.set_size(1);
-                        logrec->ids(0) = logrec->L.add_setting(prefix);
+                if ( log_level == 10 ) {
+                        logrec->ids.set_size ( 1 );
+                        logrec->ids ( 0 ) = logrec->L.add_setting ( prefix );
                 } else {
-                        // log only 
-                        logrec->ids.set_size(3);
-                        if (log_level >0){
-                                logrec->ids(0) = logrec->L.add_vector ( r, prefix + logrec->L.prefix_sep()+ "mean" );
+                        // log only
+                        logrec->ids.set_size ( 3 );
+                        if ( log_level > 0 ) {
+                                logrec->ids ( 0 ) = logrec->L.add_vector ( r, prefix + logrec->L.prefix_sep() + "mean" );
                         }
-                        if (log_level >1){
-                                logrec->ids(1) = logrec->L.add_vector ( r, prefix + logrec->L.prefix_sep()+ "lb" );
-                                logrec->ids(2) = logrec->L.add_vector ( r, prefix + logrec->L.prefix_sep()+ "ub" );
+                        if ( log_level > 1 ) {
+                                logrec->ids ( 1 ) = logrec->L.add_vector ( r, prefix + logrec->L.prefix_sep() + "lb" );
+                                logrec->ids ( 2 ) = logrec->L.add_vector ( r, prefix + logrec->L.prefix_sep() + "ub" );
                         }
                 }
         }
         void log_write() const {
-                if (log_level==10){
-                        to_setting(logrec->L.log_to_setting(logrec->ids(0)));
+                if ( log_level == 10 ) {
+                        to_setting ( logrec->L.log_to_setting ( logrec->ids ( 0 ) ) );
                 } else {
-                        if (log_level>0) {
-                                logrec->L.log_vector( logrec->ids(0), mean() );
+                        if ( log_level > 0 ) {
+                                logrec->L.log_vector ( logrec->ids ( 0 ), mean() );
                         }
-                        if (log_level>1) {
-                                vec lb; vec ub;
-                                qbounds(lb,ub);
-                                logrec->L.log_vector( logrec->ids(1), lb );
-                                logrec->L.log_vector( logrec->ids(2), ub );
+                        if ( log_level > 1 ) {
+                                vec lb;
+                                vec ub;
+                                qbounds ( lb, ub );
+                                logrec->L.log_vector ( logrec->ids ( 1 ), lb );
+                                logrec->L.log_vector ( logrec->ids ( 2 ), ub );
                         }
                 }
@@ -704 +724 @@
         //! Efficient version of samplecond
         virtual mat samplecond_mat ( const vec &cond, int N );
-        
+
         void validate() {
                 iepdf.validate();
-                if (rv._dsize()< iepdf._rv()._dsize()) {rv=iepdf._rv();};
+                if ( rv._dsize() < iepdf._rv()._dsize() ) {
+                        rv = iepdf._rv();
+                };
                 dim = iepdf.dimension();
         }
@@ -789 +811 @@
         }
         //! for future use
-        virtual ~datalink(){}
+        virtual ~datalink() {}
 };
 
@@ -829 +851 @@
                 if ( v2h_up.length() > 0 ) {
                         history.shift_right ( 0, v2h_up.length() );
-                  history.set_subvector ( 0, val_up(v2h_up) ); 
+                        history.set_subvector ( 0, val_up ( v2h_up ) );
                 }
         }
@@ -854 +876 @@
                 ivec valid_ids = rv.findself_ids ( rv_up );
                 RV rv_hist = rv.subselect ( find ( valid_ids >= 0 ) ); // select only rvs that are in rv_up
-                RV rv_hist0 =rv_hist.remove_time();  // these RVs will form history at time =0
+                RV rv_hist0 = rv_hist.remove_time(); // these RVs will form history at time =0
                 // now we need to know what is needed from Up
                 rv_hist = rv_hist.expand_delayes(); // full regressor - including time 0
-                Hrv=rv_hist.subt(rv_hist0);   // remove time 0
+                Hrv = rv_hist.subt ( rv_hist0 );   // remove time 0
                 history = zeros ( Hrv._dsize() );
 
                 // decide if we need to copy val to history
-                if (Hrv._dsize() >0) {
-                        v2h_up = rv_hist0.dataind(rv_up); // indeces of elements of rv_up to be copied
+                if ( Hrv._dsize() > 0 ) {
+                        v2h_up = rv_hist0.dataind ( rv_up ); // indeces of elements of rv_up to be copied
                 } // else v2h_up is empty
-                
+
                 Hrv.dataind ( rv, h2v_hist, h2v_down );
 
@@ -871 +893 @@
         }
         //! set history of variable given by \c rv1 to values of \c hist.
-        void set_history(const RV& rv1, const vec &hist0){
-                bdm_assert(rv1._dsize()==hist0.length(),"hist is not compatible with given rv1");
+        void set_history ( const RV& rv1, const vec &hist0 ) {
+                bdm_assert ( rv1._dsize() == hist0.length(), "hist is not compatible with given rv1" );
                 ivec ind_H;
                 ivec ind_h0;
-                Hrv.dataind(rv1, ind_H, ind_h0); // find indeces of rv in 
-                set_subvector(history, ind_H, hist0(ind_h0)); // copy given hist to appropriate places
+                Hrv.dataind ( rv1, ind_H, ind_h0 ); // find indeces of rv in
+                set_subvector ( history, ind_H, hist0 ( ind_h0 ) ); // copy given hist to appropriate places
         }
 };
@@ -957 +979 @@
         vec get_cond ( const vec &val_up, const vec &cond_up ) {
                 vec tmp ( condsize );
-                fill_cond (val_up, cond_up, tmp );
+                fill_cond ( val_up, cond_up, tmp );
                 return tmp;
         }
-        //! fill condition 
-        void fill_cond ( const vec &val_up, const vec &cond_up, vec& cond_out){
-                bdm_assert_debug(cond_out.length()>=condsize,"dl.fill_cond: cond_out is too small");
+        //! fill condition
+        void fill_cond ( const vec &val_up, const vec &cond_up, vec& cond_out ) {
+                bdm_assert_debug ( cond_out.length() >= condsize, "dl.fill_cond: cond_out is too small" );
                 set_subvector ( cond_out, v2c_lo, val_up ( v2c_up ) );
                 set_subvector ( cond_out, c2c_lo, cond_up ( c2c_up ) );
@@ -976 +998 @@
 /*! \brief Abstract class for discrete-time sources of data.
 
-The class abstracts operations of: 
-\li  data aquisition, 
-\li  data-preprocessing, such as  scaling of data, 
+The class abstracts operations of:
+\li  data aquisition,
+\li  data-preprocessing, such as  scaling of data,
 \li  data resampling from the task of estimation and control.
 Moreover, for controlled systems, it is able to receive the desired control action and perform it in the next step. (Or as soon as possible).
 
 The DataSource has three main data interaction structures:
-\li input, \f$ u_t \f$, 
+\li input, \f$ u_t \f$,
 \li output \f$ y_t \f$,
 \li data, \f$ d_t=[y_t,u_t, \ldots ]\f$ a collection of all inputs and outputs and possibly some internal variables too.
@@ -991 +1013 @@
 class DS : public root {
 protected:
-                //! size of data returned by \c getdata()
+        //! size of data returned by \c getdata()
         int dtsize;
-                //! size of data
+        //! size of data
         int utsize;
-                //!size of output
-                int ytsize;
+        //!size of output
+        int ytsize;
         //!Description of data returned by \c getdata().
         RV Drv;
         //!Description of data witten by by \c write().
         RV Urv; //
-                //!Description of output data
-                RV Yrv; //
+        //!Description of output data
+        RV Yrv; //
 public:
         //! default constructors
-        DS() : dtsize(0),utsize(0),ytsize(0),Drv(), Urv(),Yrv() {log_level=1;};
+        DS() : dtsize ( 0 ), utsize ( 0 ), ytsize ( 0 ), Drv(), Urv(), Yrv() {
+                log_level = 1;
+        };
 
         //! Returns maximum number of provided data, by default it is set to maximum allowed length, shorter DS should overload this method! See, MemDS.max_length().
-        virtual int max_length() {return std::numeric_limits< int >::max();}
+        virtual int max_length() {
+                return std::numeric_limits< int >::max();
+        }
         //! Returns full vector of observed data=[output, input]
         virtual void getdata ( vec &dt ) const {
@@ -1019 +1045 @@
 
         //! Accepts action variable and schedule it for application.
-        virtual void write (const vec &ut ) {
+        virtual void write ( const vec &ut ) {
                 bdm_error ( "abstract class" );
         }
 
         //! Accepts action variables at specific indeces
-        virtual void write (const vec &ut, const ivec &indeces ) {
+        virtual void write ( const vec &ut, const ivec &indeces ) {
                 bdm_error ( "abstract class" );
         }
 
         //! Moves from \f$ t \f$ to \f$ t+1 \f$, i.e. perfroms the actions and reads response of the system.
-        virtual void step() 
-        {
+        virtual void step() {
                 bdm_error ( "abstract class" );
         }
 
         //! Register DS for logging into logger L
-        virtual void log_register (logger &L,  const string &prefix ) {
+        virtual void log_register ( logger &L,  const string &prefix ) {
                 bdm_assert ( ytsize == Yrv._dsize(), "invalid DS: ytsize (" + num2str ( ytsize ) + ") different from Drv " + num2str ( Yrv._dsize() ) );
                 bdm_assert ( utsize == Urv._dsize(), "invalid DS: utsize (" + num2str ( utsize ) + ") different from Urv " + num2str ( Urv._dsize() ) );
 
-                root::log_register(L,prefix);
-                //we know that 
-                if (log_level >0){
-                        logrec->ids.set_size(2);
-                        logrec->ids(0) = logrec->L.add_vector ( Yrv, prefix );
-                        logrec->ids(1) = logrec->L.add_vector ( Urv, prefix );
+                root::log_register ( L, prefix );
+                //we know that
+                if ( log_level > 0 ) {
+                        logrec->ids.set_size ( 2 );
+                        logrec->ids ( 0 ) = logrec->L.add_vector ( Yrv, prefix );
+                        logrec->ids ( 1 ) = logrec->L.add_vector ( Urv, prefix );
                 }
         }
         //! Register DS for logging into logger L
         virtual void log_write ( ) const {
-                if (log_level >0) {
-                        vec tmp ( Yrv._dsize() + Urv._dsize());
+                if ( log_level > 0 ) {
+                        vec tmp ( Yrv._dsize() + Urv._dsize() );
                         getdata ( tmp );
                         // d is first in getdata
-                        logrec->L.log_vector ( logrec->ids(0), tmp.left ( Yrv._dsize() ) );
+                        logrec->L.log_vector ( logrec->ids ( 0 ), tmp.left ( Yrv._dsize() ) );
                         // u follows after d in getdata
-                        logrec->L.log_vector ( logrec->ids(1), tmp.mid ( Yrv._dsize(), Urv._dsize() ) );
+                        logrec->L.log_vector ( logrec->ids ( 1 ), tmp.mid ( Yrv._dsize(), Urv._dsize() ) );
                 }
         }
@@ -1071 +1096 @@
         }
         //! set random variables
-        virtual void set_drv (const  RV &yrv, const RV &urv) {
+        virtual void set_drv ( const  RV &yrv, const RV &urv ) {
                 Yrv = yrv;
-                Drv = concat(yrv,urv);
+                Drv = concat ( yrv, urv );
                 Urv = urv;
         }
@@ -1085 +1110 @@
 \f]
 where:
- * \f$ y_t \f$ is the variable 
+ * \f$ y_t \f$ is the variable
 Access to the resulting posterior density is via function \c posterior().
 
@@ -1109 +1134 @@
         //! size of the conditioning vector
         int dimc;
-        
+
         //!Logarithm of marginalized data likelihood.
         double ll;
@@ -1119 +1144 @@
         //! @{
 
-        BM() : yrv(),dimy(0),rvc(),dimc(0), ll ( 0 ), evalll ( true ) { };
+        BM() : yrv(), dimy ( 0 ), rvc(), dimc ( 0 ), ll ( 0 ), evalll ( true ) { };
 //      BM ( const BM &B ) :  yrv ( B.yrv ), dimy(B.dimy), rvc ( B.rvc ),dimc(B.dimc), ll ( B.ll ), evalll ( B.evalll ) {}
         //! \brief Copy function required in vectors, Arrays of BM etc. Have to be DELETED manually!
         //! Prototype: \code BM* _copy_() const {return new BM(*this);} \endcode
-        virtual BM* _copy_() const { return NULL; };
+        virtual BM* _copy_() const {
+                return NULL;
+        };
         //!@}
 
@@ -1132 +1159 @@
         @param dt vector of input data
         */
-        virtual void bayes ( const vec &yt, const vec &cond=empty_vec ) = 0;
+        virtual void bayes ( const vec &yt, const vec &cond = empty_vec ) = 0;
         //! Batch Bayes rule (columns of Dt are observations)
-        virtual void bayes_batch ( const mat &Dt, const vec &cond=empty_vec );
+        virtual void bayes_batch ( const mat &Dt, const vec &cond = empty_vec );
         //! Batch Bayes rule (columns of Dt are observations, columns of Cond are conditions)
         virtual void bayes_batch ( const mat &Dt, const mat &Cond );
         //! Evaluates predictive log-likelihood of the given data record
-        //! I.e. marginal likelihood of the data with the posterior integrated out. 
-        //! This function evaluates only \f$ y_t \f$, condition is assumed to be the last used in bayes(). 
+        //! I.e. marginal likelihood of the data with the posterior integrated out.
+        //! This function evaluates only \f$ y_t \f$, condition is assumed to be the last used in bayes().
         //! See bdm::BM::predictor for conditional version.
         virtual double logpred ( const vec &yt ) const {
@@ -1170 +1197 @@
         //! \name Access to attributes
         //!@{
-                //! access function
-                const RV& _rvc() const {
-                        return rvc;
-                }
-                //! access function
-                int dimensionc() const {
-                        return dimc;
-                }
-                //! access function
-                int dimensiony() const {
-                        return dimy;
-                }
-                //! access function
-                int dimension() const {
-                        return posterior().dimension();
-                }
-                //! access function
+        //! access function
+        const RV& _rvc() const {
+                return rvc;
+        }
+        //! access function
+        int dimensionc() const {
+                return dimc;
+        }
+        //! access function
+        int dimensiony() const {
+                return dimy;
+        }
+        //! access function
+        int dimension() const {
+                return posterior().dimension();
+        }
+        //! access function
         const RV& _yrv() const {
                 return yrv;
@@ -1196 +1223 @@
         //! access to rv of the posterior
         void set_rv ( const RV &rv ) {
-                const_cast<epdf&>(posterior()).set_rv ( rv );
+                const_cast<epdf&> ( posterior() ).set_rv ( rv );
         }
         //! access function
         void set_dim ( int dim ) {
-                const_cast<epdf&>(posterior()).set_dim ( dim );
+                const_cast<epdf&> ( posterior() ).set_dim ( dim );
         }
         //! return internal log-likelihood of the last data vector
@@ -1220 +1247 @@
         virtual void set_options ( const string &opt ) {
                 if ( opt.find ( "logfull" ) != string::npos ) {
-                        const_cast<epdf&>(posterior()).set_log_level(10) ;
+                        const_cast<epdf&> ( posterior() ).set_log_level ( 10 ) ;
                 } else {
                         if ( opt.find ( "logbounds" ) != string::npos ) {
-                                const_cast<epdf&>(posterior()).set_log_level(2) ;
+                                const_cast<epdf&> ( posterior() ).set_log_level ( 2 ) ;
                         } else {
-                                const_cast<epdf&>(posterior()).set_log_level(1) ;
+                                const_cast<epdf&> ( posterior() ).set_log_level ( 1 ) ;
                         }
                         if ( opt.find ( "logll" ) != string::npos ) {
@@ -1238 +1265 @@
         //!  * x = level of the posterior (typically 0/1/2 for nothing/mean/bounds)
         virtual void log_register ( logger &L, const string &prefix = "" ) {
-                root::log_register(L,prefix);           
-
-                const_cast<epdf&>(posterior()).log_register(L, prefix+L.prefix_sep()+"apost"); 
-                
-                if ((log_level) > 0){
-                        logrec->ids.set_size(1);
-                        logrec->ids(0) = L.add_vector(RV("",1), prefix+L.prefix_sep()+"ll");
+                root::log_register ( L, prefix );
+
+                const_cast<epdf&> ( posterior() ).log_register ( L, prefix + L.prefix_sep() + "apost" );
+
+                if ( ( log_level ) > 0 ) {
+                        logrec->ids.set_size ( 1 );
+                        logrec->ids ( 0 ) = L.add_vector ( RV ( "", 1 ), prefix + L.prefix_sep() + "ll" );
                 }
         }
@@ -1250 +1277 @@
         virtual void log_write ( ) const {
                 posterior().log_write();
-                if (log_level >0) { logrec->L.logit ( logrec->ids ( 0 ), ll );}
+                if ( log_level > 0 ) {
+                        logrec->L.logit ( logrec->ids ( 0 ), ll );
+                }
         }
         //!@}
@@ -1264 +1293 @@
                 shared_ptr<RV> r3 = UI::build<RV> ( set, "rv", UI::optional );
                 if ( r3 ) {
-                        set_rv(*r3);
-                }
-                
+                        set_rv ( *r3 );
+                }
+
                 string opt;
                 if ( UI::get ( opt, set, "options", UI::optional ) ) {

library/bdm/base/datasources.cpp

@@ -18 +18 @@
         for ( i = 0; i < indeces.length(); i++ ) {
                 j = indeces ( i );
-                dt ( i ) = Data ( rowid ( j ), time  );
+                dt ( i ) = Data ( rowid ( j ), time );
         }
 }
@@ -28 +28 @@
 }
 
-void MemDS::set_drv (const RV &drv, const RV &urv ) {
+void MemDS::set_drv ( const RV &drv, const RV &urv ) {
         bdm_assert_debug ( drv._dsize() == rowid.length(), "MemDS::set_rvs incompatible drv" );
         bdm_assert_debug ( urv._dsize() == 0, "MemDS does not support urv." );
 
-        DS::set_drv(drv,urv);
+        DS::set_drv ( drv, urv );
 }
 
-MemDS::MemDS ( mat &Dat, ivec &rowid0) : rowid ( rowid0 ) {
+MemDS::MemDS ( mat &Dat, ivec &rowid0 ) : rowid ( rowid0 ) {
         bdm_assert_debug ( max ( rowid ) <= Dat.rows(), "MemDS rowid is too high for given Dat." );
 
@@ -45 +45 @@
 //      //shift history
 //      H.shift_right ( 0, dt_size );
-// 
+//
 //      H.set_subvector ( dt_size - utsize, U ); // write U after Drv
-// 
+//
 //      //get regressor
 //      rgr = rgrlnk.pushdown ( H );
 //      // Eval Y
 //      H.set_subvector ( 0, model.samplecond ( rgr ) );
-// 
+//
 // }
-// 
+//
 // void ArxDS::from_setting ( const Setting &set ) {
 //      shared_ptr<RV> yrv = UI::build<RV> ( set, "y" , UI::compulsory );
 //      shared_ptr<RV> urv = UI::build<RV> ( set, "u" , UI::compulsory );
 //      shared_ptr<RV> rrv = UI::build<RV> ( set, "rgr" , UI::compulsory );
-// 
+//
 //      mat Th;
 //      UI::get ( Th, set, "theta", UI::compulsory );
-// 
+//
 //      vec mu0;
 //      if ( !UI::get ( mu0, set, "offset" ) )
 //              mu0 = zeros ( yrv->_dsize() );
-// 
+//
 //      mat sqR;
 //      UI::get ( sqR, set, "r", UI::compulsory );
 //      set_parameters ( Th, mu0, sqR );
 //      set_drv ( *yrv, *urv, *rrv );
-// 
+//
 //      if ( set.exists ( "opt" ) )
 //              set_options ( set["opt"] );
@@ -118 +118 @@
         time = 0;
         //rowid and delays are ignored
-        rowid = linspace(0,Data.rows()-1);
+        rowid = linspace ( 0, Data.rows() - 1 );
         set_drv ( *rvtmp, RV() );
 }
@@ -128 +128 @@
         //todo test if IM->rvc contains IM->rv
         //todo test if OM->rvc contains IM->rv
-        
-        UI::get(xt,set,"x0",UI::optional);
-        
+
+        UI::get ( xt, set, "x0", UI::optional );
+
         // prepare urv
         validate();
 }
 
-void StateDS::validate(){
-        Yrv = concat(OM->_rv() , IM->_rv()); // export also true state
+void StateDS::validate() {
+        Yrv = concat ( OM->_rv() , IM->_rv() ); // export also true state
         ytsize = Yrv._dsize();
-        
-        RV tmp=concat(OM->_rvc(), IM->_rvc()); // what i not in rvc
-        Urv = tmp.subt(Yrv); // remove dt,xt and 
-        Urv = Urv.subt(Yrv.copy_t(-1)); // remove dt,xt and 
-        utsize= Urv._dsize();
-        
-        set_drv(Yrv,Urv);
+
+        RV tmp = concat ( OM->_rvc(), IM->_rvc() ); // what i not in rvc
+        Urv = tmp.subt ( Yrv ); // remove dt,xt and
+        Urv = Urv.subt ( Yrv.copy_t ( -1 ) ); // remove dt,xt and
+        utsize = Urv._dsize();
+
+        set_drv ( Yrv, Urv );
         dtsize = utsize + ytsize;
-        
+
         dt.set_length ( dtsize );
-        if (xt.length()!= IM->dimension() ) {
-                xt=zeros(IM->dimension());
+        if ( xt.length() != IM->dimension() ) {
+                xt = zeros ( IM->dimension() );
         }
         ut.set_length ( Urv._dsize() );
-        
+
         //create data links
-        u2imc.set_connection(IM->_rvc(), Urv);
-        u2omc.set_connection(OM->_rvc(), Urv);
+        u2imc.set_connection ( IM->_rvc(), Urv );
+        u2omc.set_connection ( OM->_rvc(), Urv );
 }

library/bdm/base/datasources.h

@@ -28 +28 @@
 */
 class MemDS : public DS {
-        protected:
-                //! internal matrix of data
-                mat Data;
-                //! active column in the Data matrix
-                int time;
-                //!  vector of rows that are presented in Dt
-                ivec rowid;
-
-        public:
-                int max_length() {return Data.cols();}
-                void getdata ( vec &dt ) const;
-                void getdata ( vec &dt, const ivec &indeces );
-                void set_drv (const RV &drv,const  RV &urv );
-
-                void write ( const vec &ut ) {
-                        bdm_error ( "MemDS::write is not supported" );
+protected:
+        //! internal matrix of data
+        mat Data;
+        //! active column in the Data matrix
+        int time;
+        //!  vector of rows that are presented in Dt
+        ivec rowid;
+
+public:
+        int max_length() {
+                return Data.cols();
+        }
+        void getdata ( vec &dt ) const;
+        void getdata ( vec &dt, const ivec &indeces );
+        void set_drv ( const RV &drv, const  RV &urv );
+
+        void write ( const vec &ut ) {
+                bdm_error ( "MemDS::write is not supported" );
+        }
+
+        void write ( const vec &ut, const ivec &indices ) {
+                bdm_error ( "MemDS::write is not supported" );
+        }
+
+        void step();
+        //!Default constructor
+        MemDS () {};
+        //! Convenience constructor
+        MemDS ( mat &Dat, ivec &rowid0 );
+        /*! Create object from the following structure
+        \code
+        { class = "MemDS";
+           Data = (...);            // Data matrix or data vector
+           --- optional ---
+           drv = {class="RV"; ...} // Identification how rows of the matrix Data will be known to others
+           time = 0;               // Index of the first column to user_info,
+           rowid = [1,2,3...];     // ids of rows to be used
+        }
+        \endcode
+
+        If the optional fields are not given, they will be filled as follows:
+        \code
+        rowid= [0, 1, 2, ...number_of_rows_of_Data];
+        drv = {names=("ch0", "ch1", "ch2", ..."number_of_rows_of_Data");
+              sizes=( 1    1    1 ...);
+                  times=( 0    0    0 ...);
+                  };
+        time = 0;
+        \endcode
+        If \c rowid is given, \c drv will be named after indeces in rowids.
+
+        Hence the data provided by method \c getdata() will be full column of matrix Data starting from the first record.
+        */
+        void from_setting ( const Setting &set ) {
+                UI::get ( Data, set, "Data", UI::compulsory );
+                if ( !UI::get ( time, set, "time", UI::optional ) ) {
+                        time = 0;
                 }
-
-                void write ( const vec &ut, const ivec &indices ) {
-                        bdm_error ( "MemDS::write is not supported" );
+                if ( !UI::get ( rowid, set, "rowid", UI::optional ) ) {
+                        rowid = linspace ( 0, Data.rows() - 1 );
                 }
-
-                void step();
-                //!Default constructor
-                MemDS () {};
-                //! Convenience constructor
-                MemDS ( mat &Dat, ivec &rowid0);
-                /*! Create object from the following structure
-                \code
-                { class = "MemDS";
-                   Data = (...);            // Data matrix or data vector
-                   --- optional ---
-                   drv = {class="RV"; ...} // Identification how rows of the matrix Data will be known to others
-                   time = 0;               // Index of the first column to user_info,
-                   rowid = [1,2,3...];     // ids of rows to be used
+                shared_ptr<RV> r = UI::build<RV> ( set, "drv", UI::optional );
+                if ( !r ) {
+                        r = new RV();
+                        for ( int i = 0; i < rowid.length(); i++ ) {
+                                r->add ( RV ( "ch" + num2str ( rowid ( i ) ), 1, 0 ) );
+                        }
                 }
-                \endcode
-                
-                If the optional fields are not given, they will be filled as follows:
-                \code
-                rowid= [0, 1, 2, ...number_of_rows_of_Data];
-                drv = {names=("ch0", "ch1", "ch2", ..."number_of_rows_of_Data");
-                      sizes=( 1    1    1 ...);
-                          times=( 0    0    0 ...);
-                          };
-                time = 0;
-                \endcode
-                If \c rowid is given, \c drv will be named after indeces in rowids.
-                
-                Hence the data provided by method \c getdata() will be full column of matrix Data starting from the first record. 
-                */
-                void from_setting(const Setting &set){
-                        UI::get(Data, set, "Data", UI::compulsory);
-                        if(!UI::get(time, set,"time", UI::optional)) {time =0;}
-                        if(!UI::get(rowid, set, "rowid",UI::optional)) {rowid =linspace(0,Data.rows()-1);}
-                        shared_ptr<RV> r=UI::build<RV>(set,"drv",UI::optional);
-                        if (!r) {r=new RV();
-                                for (int i=0; i<rowid.length(); i++){ r->add(RV("ch"+num2str(rowid(i)), 1, 0));}
-                        }
-                        set_drv(*r,RV()); //empty urv
-                        dtsize=r->_dsize();
-                        ytsize = dtsize;
-                        utsize=0;
-                }
-};
-UIREGISTER(MemDS);
+                set_drv ( *r, RV() ); //empty urv
+                dtsize = r->_dsize();
+                ytsize = dtsize;
+                utsize = 0;
+        }
+};
+UIREGISTER ( MemDS );
 
 /*!  \brief Simulate data from a static pdf (epdf)
@@ -101 +110 @@
 
 class EpdfDS: public DS {
-        protected:
-                //! internal pointer to epdf from which we samplecond
-                shared_ptr<epdf> iepdf;
-                //! internal storage of data sample
-                vec dt;
-        public:
-                void step() {
-                        dt=iepdf->sample();
-                }
-                void getdata ( vec &dt_out ) const {
-                        dt_out = dt;
-                }
-                void getdata ( vec &dt_out, const ivec &ids ) {
-                        dt_out = dt ( ids );
-                }
-                const RV& _drv() const {
-                        return iepdf->_rv();
-                }
-
-                /*!
-                \code
-                class = "EpdfDS";
-                epdf = {class="epdf_offspring", ...}// uncondtitional density to sample from
-                \endcode
-
-                */
-                void from_setting ( const Setting &set ) {
-                        iepdf=UI::build<epdf> ( set,"epdf",UI::compulsory );
-                        bdm_assert(iepdf->isnamed(), "Input epdf must be named, check if RV is given correctly");
-                        dt =  zeros(iepdf->dimension());
-                        dtsize=dt.length();
-                        ytsize=dt.length();
-                        set_drv(iepdf->_rv(),RV());
-                        utsize =0;
-                        validate();
-                }
-                void validate() {
-                        dt = iepdf->sample();
-                }
+protected:
+        //! internal pointer to epdf from which we samplecond
+        shared_ptr<epdf> iepdf;
+        //! internal storage of data sample
+        vec dt;
+public:
+        void step() {
+                dt = iepdf->sample();
+        }
+        void getdata ( vec &dt_out ) const {
+                dt_out = dt;
+        }
+        void getdata ( vec &dt_out, const ivec &ids ) {
+                dt_out = dt ( ids );
+        }
+        const RV& _drv() const {
+                return iepdf->_rv();
+        }
+
+        /*!
+        \code
+        class = "EpdfDS";
+        epdf = {class="epdf_offspring", ...}// uncondtitional density to sample from
+        \endcode
+
+        */
+        void from_setting ( const Setting &set ) {
+                iepdf = UI::build<epdf> ( set, "epdf", UI::compulsory );
+                bdm_assert ( iepdf->isnamed(), "Input epdf must be named, check if RV is given correctly" );
+                dt =  zeros ( iepdf->dimension() );
+                dtsize = dt.length();
+                ytsize = dt.length();
+                set_drv ( iepdf->_rv(), RV() );
+                utsize = 0;
+                validate();
+        }
+        void validate() {
+                dt = iepdf->sample();
+        }
 };
 UIREGISTER ( EpdfDS );
@@ -146 +155 @@
 Still having only one density but allowing conditioning on either input or delayed values.
 */
-class PdfDS :public DS {
-        protected:
-                //! internal pointer to epdf from which we samplecond
-                shared_ptr<pdf> ipdf;
-                //! internal storage of data sample
-                vec yt;
-                //! input vector
-                vec ut;
-                //! datalink between ut and regressor
-                datalink_buffered ut2rgr;
-                //! datalink between yt and regressor
-                datalink_buffered yt2rgr;
-                //! numeric values of regressor
-                vec rgr;
-                
-        public:
-                void step() {
-                        yt2rgr.store_data(yt); // y is now history
-                        ut2rgr.filldown ( ut,rgr );
-                        yt2rgr.filldown ( yt,rgr );
-                        yt=ipdf->samplecond ( rgr );
-                        ut2rgr.store_data(ut); //u is now history
+class PdfDS : public DS {
+protected:
+        //! internal pointer to epdf from which we samplecond
+        shared_ptr<pdf> ipdf;
+        //! internal storage of data sample
+        vec yt;
+        //! input vector
+        vec ut;
+        //! datalink between ut and regressor
+        datalink_buffered ut2rgr;
+        //! datalink between yt and regressor
+        datalink_buffered yt2rgr;
+        //! numeric values of regressor
+        vec rgr;
+
+public:
+        void step() {
+                yt2rgr.store_data ( yt ); // y is now history
+                ut2rgr.filldown ( ut, rgr );
+                yt2rgr.filldown ( yt, rgr );
+                yt = ipdf->samplecond ( rgr );
+                ut2rgr.store_data ( ut ); //u is now history
+        }
+        void getdata ( vec &dt_out ) const {
+                bdm_assert_debug ( dt_out.length() >= utsize + ytsize, "Short output vector" );
+                dt_out.set_subvector ( 0, yt );
+                dt_out.set_subvector ( ytsize, ut );
+        }
+        void write ( const vec &ut0 ) {
+                ut = ut0;
+        }
+        void write ( const vec &ut0, const ivec &ind ) {
+                set_subvector ( ut, ind, ut0 );
+        }
+
+        /*!
+        \code
+        class = "PdfDS";
+        pdf = {class="pdf_offspring", ...};  // pdf to simulate
+        --- optional ---
+        init_rv = {class="RV",names=...};      // define what rv to initialize - typically delayed values!
+        init_values = [...];                   // vector of initial values corresponding to init_rv
+        \endcode
+
+        If init_rv is not given, init_values are set to zero.
+        */
+        void from_setting ( const Setting &set ) {
+                ipdf = UI::build<pdf> ( set, "pdf", UI::compulsory );
+
+                Yrv = ipdf->_rv();
+                // get unique rvs form rvc
+                RV rgrv0 = ipdf->_rvc().remove_time();
+                // input is what in not in Yrv
+                Urv = rgrv0.subt ( Yrv );
+                set_drv ( Yrv, Urv );
+                // connect input and output to rvc
+                ut2rgr.set_connection ( ipdf->_rvc(), Urv );
+                yt2rgr.set_connection ( ipdf->_rvc(), Yrv );
+
+                //set history - if given
+                shared_ptr<RV> rv_ini = UI::build<RV> ( set, "init_rv", UI::optional );
+                if ( rv_ini ) { // check if
+                        vec val;
+                        UI::get ( val, set, "init_values", UI::optional );
+                        if ( val.length() != rv_ini->_dsize() ) {
+                                bdm_error ( "init_rv and init_values fields have incompatible sizes" );
+                        } else {
+                                ut2rgr.set_history ( *rv_ini, val );
+                                yt2rgr.set_history ( *rv_ini, val );
+                        }
                 }
-                void getdata ( vec &dt_out ) const {
-                        bdm_assert_debug(dt_out.length()>=utsize+ytsize,"Short output vector");
-                        dt_out.set_subvector(0, yt);
-                        dt_out.set_subvector(ytsize, ut);
-                }
-                void write(const vec &ut0){ut=ut0;}
-                void write(const vec &ut0, const ivec &ind){set_subvector(ut,ind,ut0);}
-                
-                /*!
-                \code
-                class = "PdfDS";
-                pdf = {class="pdf_offspring", ...};  // pdf to simulate
-                --- optional ---
-                init_rv = {class="RV",names=...};      // define what rv to initialize - typically delayed values!
-                init_values = [...];                   // vector of initial values corresponding to init_rv
-                \endcode
-
-                If init_rv is not given, init_values are set to zero.
-                */
-                void from_setting ( const Setting &set ) {
-                        ipdf=UI::build<pdf> ( set,"pdf",UI::compulsory );
-                        
-                        Yrv = ipdf->_rv();
-                        // get unique rvs form rvc
-                        RV rgrv0=ipdf->_rvc().remove_time();
-                        // input is what in not in Yrv
-                        Urv=rgrv0.subt(Yrv); 
-                        set_drv(Yrv, Urv);
-                        // connect input and output to rvc
-                        ut2rgr.set_connection(ipdf->_rvc(), Urv); 
-                        yt2rgr.set_connection(ipdf->_rvc(), Yrv); 
-                        
-                        //set history - if given
-                        shared_ptr<RV> rv_ini=UI::build<RV>(set,"init_rv",UI::optional);
-                        if(rv_ini){ // check if 
-                                vec val;
-                                UI::get(val, set, "init_values", UI::optional);
-                                if (val.length()!=rv_ini->_dsize()){
-                                        bdm_error("init_rv and init_values fields have incompatible sizes");
-                                } else {
-                                        ut2rgr.set_history(*rv_ini, val);
-                                        yt2rgr.set_history(*rv_ini, val);
-                                }
-                        }
-
-                        yt = zeros ( ipdf->dimension() );
-                        rgr = zeros ( ipdf->dimensionc() );
-                        ut = zeros(Urv._dsize());
-
-                        ytsize=yt.length();
-                        utsize=ut.length();
-                        dtsize = ytsize+utsize;
-                        validate();
-                }
-                void validate() {
-                        //taken from sample() - shift of history is not done here
-                        ut2rgr.filldown ( ut,rgr );
-                        yt2rgr.filldown ( yt,rgr );
-                        yt=ipdf->samplecond ( rgr );
-                }
+
+                yt = zeros ( ipdf->dimension() );
+                rgr = zeros ( ipdf->dimensionc() );
+                ut = zeros ( Urv._dsize() );
+
+                ytsize = yt.length();
+                utsize = ut.length();
+                dtsize = ytsize + utsize;
+                validate();
+        }
+        void validate() {
+                //taken from sample() - shift of history is not done here
+                ut2rgr.filldown ( ut, rgr );
+                yt2rgr.filldown ( yt, rgr );
+                yt = ipdf->samplecond ( rgr );
+        }
 };
 UIREGISTER ( PdfDS );
@@ -237 +250 @@
 class FileDS: public MemDS {
 
-        public:
-                void getdata ( vec &dt ) {
-                        dt = Data.get_col ( time );
-                }
-
-                void getdata ( vec &dt, const ivec &indices ) {
-                        vec tmp = Data.get_col ( time );
-                        dt = tmp ( indices );
-                }
-
-                //! returns number of data in the file;
-                int ndat() {
-                        return Data.cols();
-                }
-                //! no sense to log this type
-                void log_register(logger &L, const string &prefix){};
-                //! no sense to log this type
-                void log_write ( ) const {};
+public:
+        void getdata ( vec &dt ) {
+                dt = Data.get_col ( time );
+        }
+
+        void getdata ( vec &dt, const ivec &indices ) {
+                vec tmp = Data.get_col ( time );
+                dt = tmp ( indices );
+        }
+
+        //! returns number of data in the file;
+        int ndat() {
+                return Data.cols();
+        }
+        //! no sense to log this type
+        void log_register ( logger &L, const string &prefix ) {};
+        //! no sense to log this type
+        void log_write ( ) const {};
 };
 
@@ -265 +278 @@
 class ITppFileDS: public FileDS {
 
-        public:
-                //! Convenience constructor
-                ITppFileDS ( const string &fname, const string &varname ) : FileDS() {
-                        it_file it ( fname );
-                        it << Name ( varname );
-                        it >> Data;
-                        time = 0;
-                        //rowid and delays are ignored
-                };
-
-                ITppFileDS () : FileDS() {
-                };
-
-                void from_setting ( const Setting &set );
-
-                // TODO dodelat void to_setting( Setting &set ) const;
+public:
+        //! Convenience constructor
+        ITppFileDS ( const string &fname, const string &varname ) : FileDS() {
+                it_file it ( fname );
+                it << Name ( varname );
+                it >> Data;
+                time = 0;
+                //rowid and delays are ignored
+        };
+
+        ITppFileDS () : FileDS() {
+        };
+
+        void from_setting ( const Setting &set );
+
+        // TODO dodelat void to_setting( Setting &set ) const;
 
 };
@@ -296 +309 @@
 class CsvFileDS: public FileDS {
 
-        public:
-                //! Constructor - create DS from a CSV file.
-                CsvFileDS ( const string& fname, const string& orientation = "BY_COL" );
+public:
+        //! Constructor - create DS from a CSV file.
+        CsvFileDS ( const string& fname, const string& orientation = "BY_COL" );
 };
 
@@ -307 +320 @@
 //! State-space data source simulating two densities
 class StateDS : public DS {
-        protected:
-                //!conditional pdf of the state evolution \f$ f(x_t|x_{t-1}) \f$
-                shared_ptr<pdf> IM;
-
-                //!conditional pdf of the observations \f$ f(d_t|x_t) \f$
-                shared_ptr<pdf> OM;
-
-                //! result storage
-                vec dt;
-                //! state storage
-                vec xt;
-                //! input storage
-                vec ut;
-
-                //! datalink from ut to IM.rvc
-                datalink_part u2imc;
-                //! datalink from ut to OM.rvc
-                datalink_part u2omc;
-        public:
-                void getdata ( vec &dt0 ) const {
-                        dt0 = dt;
-                }
-                void write (const vec &ut0 ) {
-                        ut = ut0;
-                }
-                
-                void getdata ( vec &dt0, const ivec &indices ) {
-                        dt0 = dt ( indices );
-                }
-
-                virtual void step() {
-                        vec imc(IM->dimensionc());
-                        imc.set_subvector(0,xt);
-                        u2imc.filldown(ut,imc);
-                        xt = IM->samplecond ( imc );
-                        
-                        vec omc(OM->dimensionc());
-                        omc.set_subvector(0,xt);
-                        u2omc.filldown(ut,omc);
-                        vec yt;
-                        yt = OM->samplecond ( omc );
-                        //fill all data
-                        dt.set_subvector(0,yt);
-                        dt.set_subvector(yt.length(),xt);
-                        dt.set_subvector(ytsize,ut);
-                }
-
-                //! set parameters
-                void set_parameters(shared_ptr<pdf> IM0, shared_ptr<pdf> OM0){
-                        IM=IM0;
-                        OM = OM0;
-                }
-                void set_initx(const vec &x0){xt=x0;}
-
-                /*! UI for stateDS
-
-                The DS is constructed from a structure with fields:
-                \code
-                class = "stateDS";
-                //Internal model
-                IM = { type = "pdf-offspring"; };
-                //Observation model
-                OM = { type = "pdf-offspring"; }
-                //initial state
-                x0 = [...]; //vector of data
-                \endcode
-                Both models must have defined \c rv. and \c rvc
-                Random variables not found in any rv are considered to be inputs.
-                */
-                void from_setting ( const Setting &set );
-
-                // TODO dodelat void to_setting( Setting &set ) const;
-
-                void validate();
+protected:
+        //!conditional pdf of the state evolution \f$ f(x_t|x_{t-1}) \f$
+        shared_ptr<pdf> IM;
+
+        //!conditional pdf of the observations \f$ f(d_t|x_t) \f$
+        shared_ptr<pdf> OM;
+
+        //! result storage
+        vec dt;
+        //! state storage
+        vec xt;
+        //! input storage
+        vec ut;
+
+        //! datalink from ut to IM.rvc
+        datalink_part u2imc;
+        //! datalink from ut to OM.rvc
+        datalink_part u2omc;
+public:
+        void getdata ( vec &dt0 ) const {
+                dt0 = dt;
+        }
+        void write ( const vec &ut0 ) {
+                ut = ut0;
+        }
+
+        void getdata ( vec &dt0, const ivec &indices ) {
+                dt0 = dt ( indices );
+        }
+
+        virtual void step() {
+                vec imc ( IM->dimensionc() );
+                imc.set_subvector ( 0, xt );
+                u2imc.filldown ( ut, imc );
+                xt = IM->samplecond ( imc );
+
+                vec omc ( OM->dimensionc() );
+                omc.set_subvector ( 0, xt );
+                u2omc.filldown ( ut, omc );
+                vec yt;
+                yt = OM->samplecond ( omc );
+                //fill all data
+                dt.set_subvector ( 0, yt );
+                dt.set_subvector ( yt.length(), xt );
+                dt.set_subvector ( ytsize, ut );
+        }
+
+        //! set parameters
+        void set_parameters ( shared_ptr<pdf> IM0, shared_ptr<pdf> OM0 ) {
+                IM = IM0;
+                OM = OM0;
+        }
+        void set_initx ( const vec &x0 ) {
+                xt = x0;
+        }
+
+        /*! UI for stateDS
+
+        The DS is constructed from a structure with fields:
+        \code
+        class = "stateDS";
+        //Internal model
+        IM = { type = "pdf-offspring"; };
+        //Observation model
+        OM = { type = "pdf-offspring"; }
+        //initial state
+        x0 = [...]; //vector of data
+        \endcode
+        Both models must have defined \c rv. and \c rvc
+        Random variables not found in any rv are considered to be inputs.
+        */
+        void from_setting ( const Setting &set );
+
+        // TODO dodelat void to_setting( Setting &set ) const;
+
+        void validate();
 };
 

library/bdm/base/loggers.cpp

@@ -22 +22 @@
                 // avoid uninitialized memory
                 for ( int j = 0; j < vectors ( i ).rows(); ++j ) {
-                        for (int k = 0; k < vectors ( i ).cols(); ++k ) {
-                                vectors ( i )(j, k) = 0;
+                        for ( int k = 0; k < vectors ( i ).cols(); ++k ) {
+                                vectors ( i ) ( j, k ) = 0;
                         }
                 }
@@ -49 +49 @@
 void memlog::from_setting ( const Setting &set ) {
         // TODO tady se natvrdo ocekava existence stringu, nejsou zadne defaulty.. je to tak OK?
-        UI::get(maxlen,  set,"maxlen",UI::compulsory);
-        UI::get(filename,set,"filename");
+        UI::get ( maxlen,  set, "maxlen", UI::compulsory );
+        UI::get ( filename, set, "filename" );
 }
 

library/bdm/base/loggers.h

@@ -36 +36 @@
 public:
         //! convenience constructor
-        memlog ( int maxlen0, string fn = "" ) :logger("_"), maxlen ( maxlen0 ), ind ( 0 ), vectors ( 0 ), filename ( fn ) {}
+        memlog ( int maxlen0, string fn = "" ) : logger ( "_" ), maxlen ( maxlen0 ), ind ( 0 ), vectors ( 0 ), filename ( fn ) {}
 
         //!Default constructor
-        memlog() : logger("_"), maxlen ( 0 ), ind ( 0 ), vectors ( 0 ) {}
+        memlog() : logger ( "_" ), maxlen ( 0 ), ind ( 0 ), vectors ( 0 ) {}
 
         //! Initialize storage
@@ -67 +67 @@
         void finalize() {
                 if ( filename.length() > 0 ) {
-                        itsave ( (filename+".it").c_str());
-                        if (settings.length()>0){
-                                setting_conf.writeFile( (filename+".cfg").c_str());
+                        itsave ( ( filename + ".it" ).c_str() );
+                        if ( settings.length() > 0 ) {
+                                setting_conf.writeFile ( ( filename + ".cfg" ).c_str() );
                         }
                 }
-                
+
         };
 
@@ -100 +100 @@
 All data records are written out to std from where they could be send to file
 */
-class stdlog: public memlog{
-        public:
-                //! default constructor
-                stdlog():memlog(1){};
-                
-                void init() {
-                        memlog::init();
-                        for (int i=0; i<entries.length();i++){
-                                if (entries(i)._dsize()==1) {
-                                        cout << names(i) << entries(i).name(0) << "\t";
+class stdlog: public memlog {
+public:
+        //! default constructor
+        stdlog() : memlog ( 1 ) {};
+
+        void init() {
+                memlog::init();
+                for ( int i = 0; i < entries.length(); i++ ) {
+                        if ( entries ( i )._dsize() == 1 ) {
+                                cout << names ( i ) << entries ( i ).name ( 0 ) << "\t";
+                        } else
+                                for ( int j = 0; j < vectors ( i ).cols(); j++ ) {
+                                        cout << names ( i ) << entries ( i ).scalarname ( j ) << "\t";
                                 }
-                                else
-                                for (int j=0; j<vectors(i).cols(); j++){
-                                        cout << names(i) << entries(i).scalarname(j) << "\t";
-                                }
+                }
+                cout << endl;
+
+
+        }
+        //!writes everything out
+        void step() {
+                for ( int i = 0; i < vectors.length(); i++ ) {
+                        for ( int j = 0; j < vectors ( i ).cols(); j++ ) {
+                                cout << vectors ( i ) ( 0, j ) << "\t";
                         }
-                        cout << endl;
-                        
-                        
                 }
-                //!writes everything out
-                void step() {
-                        for (int i=0; i<vectors.length();i++){
-                                for (int j=0; j<vectors(i).cols(); j++){
-                                        cout << vectors(i)(0,j) << "\t";
-                                }
-                        }
-                        cout << endl;
-                }
-                /*! \brief UI for stdlog
-                
-                TODO dat tam kam patri, a to celej blok
-                
-                \code
-                logger = {
-                        class = "stdlog"; // no parameterization needed
-                }
-                \endcode
-                */
-                void from_setting ( const Setting &set ){
-                }
-                
+                cout << endl;
+        }
+        /*! \brief UI for stdlog
+
+        TODO dat tam kam patri, a to celej blok
+
+        \code
+        logger = {
+                class = "stdlog"; // no parameterization needed
+        }
+        \endcode
+        */
+        void from_setting ( const Setting &set ) {
+        }
+
 };
-UIREGISTER(stdlog);
+UIREGISTER ( stdlog );
 
 /*!

library/bdm/base/user_info.cpp

@@ -15 +15 @@
 namespace bdm {
 
-string UIException::format_message( const string &reason, const string &path ) {
+string UIException::format_message ( const string &reason, const string &path ) {
         stringstream ss;
         ss << reason;
@@ -78 +78 @@
 void UI::MappedUI::add_class ( const string &class_name, const type_info * const class_type_info, const UI* const ui ) {
         pair< StringToUIMap::iterator, bool> inres =
-                mapped_strings().insert (
-                        StringToUIMap::value_type( class_name, ui ) );
+            mapped_strings().insert (
+                StringToUIMap::value_type ( class_name, ui ) );
         if ( inres.second ) {
                 mapped_type_infos().insert (
-                        TypeInfoToStringMap::value_type (
-                                class_type_info, class_name ) );
+                    TypeInfoToStringMap::value_type (
+                        class_type_info, class_name ) );
         }
 }
@@ -198 +198 @@
                        : element.add ( name, Setting::TypeList );
 
-                                   Setting &tag= set.add ( Setting::TypeString );
-                                   tag ="matrix";
-                                   
+        Setting &tag = set.add ( Setting::TypeString );
+        tag = "matrix";
+
         Setting &cols = set.add ( Setting::TypeInt );
         cols = matrix.cols();
@@ -310 +310 @@
                 from_setting ( matrix, link.result );
 
-                if ( matrix.cols() != 1 && matrix.rows() != 1 && matrix.cols()!=0)
+                if ( matrix.cols() != 1 && matrix.rows() != 1 && matrix.cols() != 0 )
                         throw UISettingException ( "UIException: the vector length is invalid, it seems to be rather a matrix.", link.result );
 

library/bdm/base/user_info.h

@@ -48 +48 @@
         */
         UIException ( const string &message ) :
-                message ( message ) {
+                        message ( message ) {
         }
 
@@ -63 +63 @@
           Setting path in addition to the message.
         */
-        static string format_message( const string &reason, const string &path );
+        static string format_message ( const string &reason, const string &path );
 };
 
@@ -72 +72 @@
 public:
         //! Use this constructor when you can pass the problematical Setting as a parameter
-        UISettingException ( const string &message, const Setting &element ):
-                UIException ( format_message ( message, string ( element.getPath() ) ) ) {
+        UISettingException ( const string &message, const Setting &element ) :
+                        UIException ( format_message ( message, string ( element.getPath() ) ) ) {
         }
 
         //! This constructor is for other occasions, when only path of problematical Setting is known
-        UISettingException ( const string &message, const string &path ):
-                UIException ( format_message ( message, path ) ) {
+        UISettingException ( const string &message, const string &path ) :
+                        UIException ( format_message ( message, path ) ) {
         }
 
@@ -90 +90 @@
 public:
         //! Use this constructor when you can pass the problematical Setting as a parameter
-        UIClassException ( const string &message, const Setting &element ):
-                UIException ( format_message ( message, string ( element.getPath() ) ) ) {
+        UIClassException ( const string &message, const Setting &element ) :
+                        UIException ( format_message ( message, string ( element.getPath() ) ) ) {
         }
 
         //! This constructor is for other occasions, when only path of problematical Setting is known
-        UIClassException ( const string &message, const string &path ):
-                UIException ( format_message ( message, path ) ) {
+        UIClassException ( const string &message, const string &path ) :
+                        UIException ( format_message ( message, path ) ) {
         }
 
@@ -337 +337 @@
                         msg += class_name;
                         msg += ".from_setting(Setting&) has thrown a SettingException.";
-                        throw UISettingException(msg, sttng_xcptn.getPath());
-                } catch (std::runtime_error &e) {
+                        throw UISettingException ( msg, sttng_xcptn.getPath() );
+                } catch ( std::runtime_error &e ) {
                         delete instance;
                         instance = 0;
@@ -345 +345 @@
                         msg += " says: ";
                         msg += e.what();
-                        throw UISettingException(msg, link.result);
-                } catch (...) {
+                        throw UISettingException ( msg, link.result );
+                } catch ( ... ) {
                         delete instance;
                         instance = 0;
                         throw;
                 }
-}
+        }
 
         //! This method converts a Setting into a descendant of class
@@ -383 +383 @@
         template<class T> static void from_setting ( T &variable_to_load, const Setting &element ) {
                 std::string msg = "UIException: from_setting is not implemented for type ";
-                msg += typeid(T).name();
+                msg += typeid ( T ).name();
                 msg += '.';
                 throw UISettingException ( msg, element );
@@ -441 +441 @@
         }
 
-//! The new instance of type T* is constructed and initialized with values stored in the given Setting 
+//! The new instance of type T* is constructed and initialized with values stored in the given Setting
 //!
 //! Handy in mex files. Use with care.
-template<class T>
-static shared_ptr<T> build ( const Setting &element, SettingPresence settingPresence = optional ) {     
-        shared_ptr<T> instance;
-        from_setting<T> ( instance,  element  );
-        return instance;
-}
+        template<class T>
+        static shared_ptr<T> build ( const Setting &element, SettingPresence settingPresence = optional ) {
+                shared_ptr<T> instance;
+                from_setting<T> ( instance,  element );
+                return instance;
+        }
 
         //!@}
@@ -481 +481 @@
                                 stream << "UIException: the compulsory Setting with the index " << index << " is missing.";
                                 stream << index;
-                                throw UISettingException (stream.str(), element );
+                                throw UISettingException ( stream.str(), element );
                         }
                 }
@@ -560 +560 @@
                         msg += class_name;
                         msg += ".to_setting(Setting&) has thrown a SettingException.";
-                        throw UISettingException(msg, sttng_xcptn.getPath());
+                        throw UISettingException ( msg, sttng_xcptn.getPath() );
                 }
         }
@@ -597 +597 @@
 
         //! for future use
-        virtual ~UI(){}
+        virtual ~UI() {}
 };
 
@@ -645 +645 @@
 #define UIREGISTER2(class_name, temp_name) static bdm::ParticularUI<class_name<temp_name> > UI##class_name##_##temp_name( QUOTEME(class_name<temp_name>) )
 #else
-#define UIREGISTER2(class_name,temp_name) 
+#define UIREGISTER2(class_name,temp_name)
 #endif