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MAl_Readonly Class Reference

#include <mal_readonly.h>

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Public Member Functions

 MAl_Readonly (size_t bufsize, std::set< db_recno_t > &recnolist, TrapperDoc *pdoc)
virtual ~MAl_Readonly ()
void print_info (size_t ID)
size_t get_num_seq ()
std::string get_name (size_t ID)
std::string get_header (size_t ID)
std::string get_seq (size_t ID)
std::string get_strand (size_t ID)
size_t get_len (size_t ID)
void select_read (size_t ID, bool status)
size_t get_seq_row (size_t ID)
size_t get_seq_begin (size_t ID)
size_t get_seq_begin_global (size_t ID)
size_t get_seq_end (size_t ID)
size_t get_seq_end_global (size_t ID)
size_t get_beginGood (size_t ID)
size_t get_beginGood_global (size_t ID)
size_t get_endGood (size_t ID)
size_t get_endGood_global (size_t ID)
base_t get_base (size_t ID, size_t index)
base_t get_base_global (size_t ID, size_t index)
qual_t get_qual (size_t ID, size_t index)
qual_t get_qual_global (size_t ID, size_t index)
bool is_DNP (size_t ID, size_t index)
bool is_DNP_global (size_t ID, size_t index)
int get_DNP_ID (size_t ID, size_t index)
int get_DNP_ID_global (size_t ID, size_t index)
int get_DNP_type (size_t ID, size_t index)
int get_DNP_type_global (size_t ID, size_t index)

Protected Member Functions

size_t get_buffID (size_t ID)
size_t next_buffID ()
virtual void flush_buffer (size_t buffID)
void read_from_db (size_t buffID, size_t ID)
void read_seq_from_db (db_recno_t recno, size_t buffID)
void read_feat_from_db (db_recno_t recno, size_t buffID, const string &data_type_name)

Protected Attributes

size_t buff_size
size_t num_seq
TrapperDoc * doc
std::set< db_recno_t > & selectedReads
std::vector< std::vector<
base_t > > 		seqs
std::vector< std::vector<
qual_t > > 		quals
std::vector< std::vector<
dnp_struct > > 		DNPs
std::vector< std::string > names
std::vector< std::string > headers
std::vector< std::string > mates
std::vector< std::string > strands
std::vector< size_t > seq_rows
std::vector< size_t > seq_begin_global
std::vector< size_t > seq_end_global
std::vector< size_t > seq_beginGood
std::vector< size_t > seq_endGood
std::vector< size_t > mate_lengths
vector< db_recno_t > ID_to_dbID
vector< size_t > ID_to_buffID
vector< db_recno_t > buffID_to_dbID
vector< db_recno_t > buffID_to_ID
vector< bool > put_in_db

Classes

struct  dnp_struct

Detailed Description

Definition at line 42 of file mal_readonly.h.

Constructor & Destructor Documentation

MAl_Readonly::MAl_Readonly (  size_t  bufsize,
std::set< db_recno_t > &  recnolist,
TrapperDoc *  pdoc
) 
 

MAl_Readonly::~MAl_Readonly (   )  [virtual]
 

Definition at line 76 of file mal_readonly.cc.

00077 {
00078   //Nothing to be done here...
00079 }

Member Function Documentation

void MAl_Readonly::flush_buffer (  size_t  buffID  )  [protected, virtual]
 

Reimplemented in MAl.

Definition at line 376 of file mal_readonly.cc.

Referenced by get_buffID().

00377 {
00378   //Not implemented in read only MAl
00379   
00380 }

base_t MAl_Readonly::get_base (  size_t  ID,
size_t  index
) 
 

Definition at line 232 of file mal_readonly.cc.

References get_buffID(), and seqs.

Referenced by get_base_global(), MAlWrapper< alphabet >::operator()(), SubsetAlgo::start(), and PrintAlgo::start().

00233 {
00234   
00235   ID = get_buffID( ID );
00236   
00237   assert( ID < seqs.size() );
00238 
00239   if (index >= seqs[ ID ].size() ) {
00240     cout << flush;
00241     cerr << "index (local) = " << index << ", seqs[ ID ].size() = " << seqs[ ID ].size() << endl;
00242 
00243   }
00244   assert( index < seqs[ ID ].size() );
00245   
00246   base_t tmp = seqs[ ID ][ index ];
00247   if (tmp == '*')
00248     tmp = '-';
00249 
00250   return tmp;
00251 //  return seqs[ ID ][ index ];
00252 }

base_t MAl_Readonly::get_base_global (  size_t  ID,
size_t  index
) 
 

Definition at line 254 of file mal_readonly.cc.

References get_base(), and get_seq_begin_global().

Referenced by MAl_addon::get_entry(), and MAl_addon::MAl_addon().

00255 {
00256   return get_base( ID, index - get_seq_begin_global( ID ) );
00257   
00258 }

size_t MAl_Readonly::get_beginGood (  size_t  ID  ) 
 

Definition at line 201 of file mal_readonly.cc.

References get_buffID(), and seq_beginGood.

Referenced by get_beginGood_global(), MAl::insert_gap(), and MAl::remove_gap().

00202 {
00203   ID = get_buffID( ID );
00204 
00205   assert( ID < seq_beginGood.size() );
00206   
00207   return seq_beginGood[ ID ];
00208 }

size_t MAl_Readonly::get_beginGood_global (  size_t  ID  ) 
 

Definition at line 210 of file mal_readonly.cc.

References get_beginGood(), and get_seq_begin_global().

Referenced by MAl_addon::get_row_start(), and MAl_addon::MAl_addon().

00211 {
00212   return get_beginGood( ID ) + get_seq_begin_global( ID );
00213   
00214 }

size_t MAl_Readonly::get_buffID (  size_t  ID  )  [protected]
 

Definition at line 328 of file mal_readonly.cc.

References flush_buffer(), ID_to_buffID, next_buffID(), put_in_db, and read_from_db().

Referenced by MAl::create_seq(), get_base(), get_beginGood(), get_DNP_ID(), get_DNP_type(), get_endGood(), get_header(), get_len(), get_name(), get_qual(), get_seq(), get_seq_begin_global(), get_seq_end_global(), get_seq_row(), get_strand(), MAl::insert_gap(), is_DNP(), MAl::remove_gap(), MAl::set_base(), MAl::set_beginGood(), MAl::set_DNP(), MAl::set_DNP_ID(), MAl::set_DNP_type(), MAl::set_endGood(), MAl::set_qual(), MAl::set_seq_begin_global(), MAl::set_seq_end_global(), and MAl::set_seq_row().

00329 {
00330   
00331 
00332   assert( ID < ID_to_buffID.size() );
00333   size_t buffID = ID_to_buffID[ ID ];
00334 
00335   if ( buffID == 0 ) {
00336     //Seq is not present in buffer and thus has to be read into buffer,
00337     //OR a new seq is being created
00338     buffID = next_buffID();
00339 
00340     if ( buffID >= put_in_db.size() ) {
00341       cerr<<"buffID: "<<buffID<<endl;
00342       cerr<<"put_in_db.size(): "<<put_in_db.size()<<endl;
00343     }
00344     
00345     assert( buffID < put_in_db.size() );
00346     
00347     if ( put_in_db[ buffID ] ) {
00348       
00349       flush_buffer( buffID );
00350     }
00351     
00352     //If dbID is 0, a new seq is being created and nothing has to be read from DB
00353     //This is taken care of in read_from_db()
00354 
00355     read_from_db( buffID, ID );
00356 
00357     
00358   }
00359   assert( buffID != 0 );
00360   return buffID;
00361 
00362 }

int MAl_Readonly::get_DNP_ID (  size_t  ID,
size_t  index
) 
 

Definition at line 295 of file mal_readonly.cc.

References DNPs, and get_buffID().

Referenced by get_DNP_ID_global(), and DnpSortAlgo::init().

00296 {
00297   ID = get_buffID( ID );
00298 
00299   assert( ID < DNPs.size() );
00300   assert( index < DNPs[ ID ].size() );
00301   
00302   return DNPs[ ID ][ index ].ID;  
00303 }

int MAl_Readonly::get_DNP_ID_global (  size_t  ID,
size_t  index
) 
 

Definition at line 305 of file mal_readonly.cc.

References get_DNP_ID(), and get_seq_begin_global().

00306 {
00307   return get_DNP_ID( ID, index - get_seq_begin_global( ID ) ); 
00308 }

int MAl_Readonly::get_DNP_type (  size_t  ID,
size_t  index
) 
 

Definition at line 310 of file mal_readonly.cc.

References DNPs, and get_buffID().

Referenced by get_DNP_type_global().

00311 {
00312   ID = get_buffID( ID );
00313 
00314   assert( ID < DNPs.size() );
00315   assert( index < DNPs[ ID ].size() );
00316   
00317   return DNPs[ ID ][ index ].type;
00318 }

int MAl_Readonly::get_DNP_type_global (  size_t  ID,
size_t  index
) 
 

Definition at line 320 of file mal_readonly.cc.

References get_DNP_type(), and get_seq_begin_global().

00321 {
00322   return get_DNP_type( ID, index - get_seq_begin_global( ID ) );  
00323 }

size_t MAl_Readonly::get_endGood (  size_t  ID  ) 
 

Definition at line 217 of file mal_readonly.cc.

References get_buffID(), and seq_endGood.

Referenced by get_endGood_global(), MAl::insert_gap(), and MAl::remove_gap().

00218 {
00219   ID = get_buffID( ID );
00220 
00221   assert( ID < seq_endGood.size() );
00222   
00223   return seq_endGood[ ID ];
00224   
00225 }

size_t MAl_Readonly::get_endGood_global (  size_t  ID  ) 
 

Definition at line 227 of file mal_readonly.cc.

References get_endGood(), and get_seq_begin_global().

Referenced by MAl_addon::get_row_end(), and MAl_addon::MAl_addon().

00228 {
00229   return get_endGood( ID ) + get_seq_begin_global( ID );
00230 }

std::string MAl_Readonly::get_header (  size_t  ID  ) 
 

Definition at line 99 of file mal_readonly.cc.

References get_buffID(), and headers.

00100 {
00101   ID = get_buffID( ID );
00102   
00103   assert( ID < headers.size() );
00104   
00105   return headers[ ID ];
00106   
00107 }

size_t MAl_Readonly::get_len (  size_t  ID  ) 
 

Definition at line 130 of file mal_readonly.cc.

References get_buffID(), and seqs.

Referenced by print_info(), SubsetAlgo::start(), RemoveAlgo::start(), and DnpSearchAlgo::start().

00131 {
00132   ID = get_buffID( ID );
00133   
00134   assert( ID < seqs.size() );
00135   
00136   return seqs[ ID ].size();
00137   
00138 }

std::string MAl_Readonly::get_name (  size_t  ID  ) 
 

Definition at line 89 of file mal_readonly.cc.

References get_buffID(), and names.

Referenced by SubsetAlgo::start(), ReadnamesAlgo::start(), and AceWriter::write_ace_file().

00090 {
00091   ID = get_buffID( ID );
00092   
00093   assert( ID < names.size() );
00094   
00095   return names[ ID ];
00096   
00097 }

size_t MAl_Readonly::get_num_seq (   ) 
 

Definition at line 84 of file mal_readonly.cc.

References num_seq.

Referenced by MAl_addon::get_num_rows(), DnpSortAlgo::init(), MAl_addon::MAl_addon(), MAlWrapper< alphabet >::nrows(), SortAlgo::old_start(), TrashRemoveAlgo::start(), TrashAlgo::start(), SubsetAlgo::start(), StrandsAlgo::start(), SortAlgo::start(), RemoveAlgo::start(), ReadnamesAlgo::start(), ReadListAlgo::start(), PrintAlgo::start(), DnpSearchAlgo::start(), and AceWriter::write_ace_file().

00085 {
00086   return num_seq;
00087 }

qual_t MAl_Readonly::get_qual (  size_t  ID,
size_t  index
) 
 

Definition at line 260 of file mal_readonly.cc.

References get_buffID(), and quals.

Referenced by TrashAlgo::check_qual_in_win(), get_qual_global(), and SubsetAlgo::start().

00261 {
00262   ID = get_buffID( ID );
00263   
00264   assert( ID < quals.size() );
00265   assert( index < quals[ ID ].size() );
00266   
00267   return quals[ ID ][ index ];
00268   
00269 }

qual_t MAl_Readonly::get_qual_global (  size_t  ID,
size_t  index
) 
 

Definition at line 271 of file mal_readonly.cc.

References get_qual(), and get_seq_begin_global().

Referenced by MAl_addon::get_qual().

00272 {
00273   
00274   return get_qual( ID, index - get_seq_begin_global( ID ) );
00275   
00276 }

std::string MAl_Readonly::get_seq (  size_t  ID  ) 
 

Definition at line 109 of file mal_readonly.cc.

References get_buffID(), and seqs.

00110 {
00111   ID = get_buffID( ID );
00112   
00113   assert( ID < seqs.size() );
00114   
00115 //   return seqs[ ID ];
00116   return string(seqs[ ID ].begin(), seqs[ ID ].end());
00117   
00118 }

size_t MAl_Readonly::get_seq_begin (  size_t  ID  ) 
 

size_t MAl_Readonly::get_seq_begin_global (  size_t  ID  ) 
 

Definition at line 172 of file mal_readonly.cc.

References get_buffID(), and seq_begin_global.

Referenced by MAlWrapper< alphabet >::decrement_first_pos(), MAlWrapper< alphabet >::first_pos(), get_base_global(), get_beginGood_global(), get_DNP_ID_global(), get_DNP_type_global(), get_endGood_global(), get_qual_global(), get_seq_end(), MAl::insert_gap_global(), is_DNP_global(), MAlWrapper< alphabet >::move_read_left(), MAlWrapper< alphabet >::move_read_right(), SortAlgo::old_start(), print_info(), MAl::remove_gap_global(), MAl::set_base_global(), MAl::set_beginGood_global(), MAl::set_DNP_global(), MAl::set_DNP_ID_global(), MAl::set_DNP_type_global(), MAl::set_endGood_global(), MAl::set_qual_global(), MAl::set_seq_end(), SortAlgo::start(), and PrintAlgo::start().

00174 {
00175   ID = get_buffID( ID );
00176 
00177   assert( ID < seq_begin_global.size() );
00178   
00179   return seq_begin_global[ ID ];
00180                            
00181 }

size_t MAl_Readonly::get_seq_end (  size_t  ID  ) 
 

Definition at line 184 of file mal_readonly.cc.

References get_seq_begin_global(), and get_seq_end_global().

Referenced by DnpSortAlgo::init(), MAl::insert_gap(), MAl::remove_gap(), PrintAlgo::start(), and TrashAlgo::trash().

00185 {
00186   
00187   return get_seq_end_global( ID ) - get_seq_begin_global( ID );
00188 }

size_t MAl_Readonly::get_seq_end_global (  size_t  ID  ) 
 

Definition at line 190 of file mal_readonly.cc.

References get_buffID(), and seq_end_global.

Referenced by MAlWrapper< alphabet >::adjust_last_pos(), MAlWrapper< alphabet >::decrement_last_pos(), MAlWrapper< alphabet >::erase(), get_seq_end(), MAlWrapper< alphabet >::insert(), MAlWrapper< alphabet >::last_pos(), MAlWrapper< alphabet >::move_read_left(), MAlWrapper< alphabet >::move_read_right(), SortAlgo::old_start(), print_info(), and SortAlgo::start().

00191 {
00192   ID = get_buffID( ID );
00193 
00194   assert( ID < seq_end_global.size() );
00195   
00196   return seq_end_global[ ID ];
00197   
00198 }

size_t MAl_Readonly::get_seq_row (  size_t  ID  ) 
 

Definition at line 161 of file mal_readonly.cc.

References get_buffID(), and seq_rows.

00162 {
00163   ID = get_buffID( ID );
00164 
00165   assert( ID < seq_rows.size() );
00166   
00167   return seq_rows[ ID ];
00168   
00169 }

string MAl_Readonly::get_strand (  size_t  ID  ) 
 

Definition at line 120 of file mal_readonly.cc.

References get_buffID(), and strands.

00121 {
00122   ID = get_buffID( ID );
00123   
00124   assert( ID < strands.size() );
00125   
00126   return strands[ ID ];
00127   
00128 }

bool MAl_Readonly::is_DNP (  size_t  ID,
size_t  index
) 
 

Definition at line 279 of file mal_readonly.cc.

References DNPs, and get_buffID().

Referenced by is_DNP_global(), and AceWriter::write_ace_file().

00280 {
00281   ID = get_buffID( ID );
00282 
00283   assert( ID < DNPs.size() );
00284   assert( index < DNPs[ ID ].size() );
00285   
00286   return DNPs[ ID ][ index ].isDNP;
00287 }

bool MAl_Readonly::is_DNP_global (  size_t  ID,
size_t  index
) 
 

Definition at line 289 of file mal_readonly.cc.

References get_seq_begin_global(), and is_DNP().

Referenced by MAl_addon::is_DNP().

00290 {
00291 
00292   return is_DNP( ID, index - get_seq_begin_global( ID ) );
00293 }

size_t MAl_Readonly::next_buffID (   )  [protected]
 

Definition at line 364 of file mal_readonly.cc.

Referenced by get_buffID().

00365 {
00366 //   static size_t curr_buffID(static_cast<size_t>(-1));//Have to check this, but should work although size_t is unsigned
00367   static size_t curr_buffID(0);//ID == 0 is unused...
00368   ++curr_buffID;
00369   
00370   if ( curr_buffID == buff_size ) curr_buffID = 1;
00371   
00372   return curr_buffID;
00373   
00374 }

void MAl_Readonly::print_info (  size_t  ID  )  [inline]
 

Definition at line 52 of file mal_readonly.h.

References get_len(), get_seq_begin_global(), and get_seq_end_global().

Referenced by MAlWrapper< alphabet >::print_info().

00052                              {
00053     cerr << "mal_readonly: print_info: ID = " << ID << endl;
00054     cerr << "get_seq_begin_global( ID ) = " << get_seq_begin_global( ID ) << endl;
00055     cerr << "get_seq_end_global( ID ) = " << get_seq_end_global( ID ) << endl;
00056     cerr << "get_len( ID ) = " << get_len( ID ) << endl;
00057   }

void MAl_Readonly::read_feat_from_db (  db_recno_t  recno,
size_t  buffID,
const string &  data_type_name
)  [protected]
 

Definition at line 442 of file mal_readonly.cc.

References Database::SecondaryIterator< T >::answer(), DNPs, doc, Database::SecondaryIterator< T >::key(), Database::SecondaryIterator< T >::nextdup(), quals, seqs, Database::SecondaryIterator< T >::set(), and FeatureData::setReadRecno().

Referenced by read_from_db().

00443 {
00444   Database::SecondaryIterator<FeatureData> feat_it("readRecno", doc, data_type_name);
00445   
00446   feat_it.key()->setReadRecno( recno );
00447 
00448   if ( feat_it.set() != 0 ) {
00449 //     cerr<<"MAl_Readonly::read_feat_from_db(): No "<<data_type_name<<" for read with recno "<<recno<<endl;
00450     return;
00451   }
00452 
00453 //   cerr<<"MAl_Readonly::read_feat_from_db(): Reading feature "<<data_type_name<<endl;
00454   
00455   if ( DnaStrData* data = dynamic_cast<DnaStrData*>(feat_it.answer()) ) {
00456     seqs[buffID] = data->dnaVector.stlVector();
00457     //Have to init DNPs here to assert that DNP vec is of same size...
00458     DNPs[buffID] = vector<dnp_struct>(seqs[buffID].size(), dnp_struct());
00459   }
00460   else if ( QualityData* data = dynamic_cast<QualityData*>(feat_it.answer()) ) {
00461     quals[buffID] = data->qualityVector.stlVector();
00462   }
00463   else if ( DnpData* data = dynamic_cast<DnpData*>(feat_it.answer()) ) {
00464     
00465     do {
00466 //       cerr<<"Found DNP at position "<<data->startPos()<<endl;
00467       DNPs[buffID][ data->startPos() ].isDNP = true;
00468       DNPs[buffID][ data->startPos() ].recno = data->getRecno();
00469       DNPs[buffID][ data->startPos() ].ID = data->get_dnpID();      
00470       DNPs[buffID][ data->startPos() ].type = data->get_dnp_type();      
00471       
00472     } while ( (feat_it.nextdup() == 0) && (data = dynamic_cast<DnpData*>(feat_it.answer())) );
00473   }
00474   
00475   
00476 }

void MAl_Readonly::read_from_db (  size_t  buffID,
size_t  ID
)  [protected]
 

Definition at line 382 of file mal_readonly.cc.

References buffID_to_dbID, buffID_to_ID, ID_to_buffID, ID_to_dbID, put_in_db, read_feat_from_db(), and read_seq_from_db().

Referenced by get_buffID().

00383 {
00384 
00385   db_recno_t recno = ID_to_dbID[ ID ];
00386 
00387   if ( recno != 0 ) {
00388 
00389     //NB: EXTREMELY important that DNP features and other features
00390     //that appear more than once on reads are read AFTER DnaStrData!!!
00391 
00392     read_seq_from_db( recno, buffID );
00393     read_feat_from_db( recno, buffID, "DnaStrData");//The seq
00394     read_feat_from_db( recno, buffID, "QualityData");//The qual
00395     read_feat_from_db( recno, buffID, "DnpData");//The dnps
00396     
00397     
00398     /*
00399       read_feat_from_db( recno, buffID, "beginGood");//Maybe this should be added as data in the seq class...
00400       read_feat_from_db( recno, buffID, "endGood");//Ditto
00401       read_feat_from_db( recno, buffID, "name");//Ditto
00402       read_feat_from_db( recno, buffID, "header");//Ditto
00403       read_feat_from_db( recno, buffID, "strand");//Ditto
00404       
00405     */
00406     
00407   }
00408   
00409 
00410   ID_to_buffID[ ID ] = buffID;
00411   buffID_to_dbID[ buffID ] = recno;
00412   buffID_to_ID[ buffID ] = ID;
00413   put_in_db[ buffID ] = true;
00414 }

void MAl_Readonly::read_seq_from_db (  db_recno_t  recno,
size_t  buffID
)  [protected]
 

Definition at line 416 of file mal_readonly.cc.

References Database::PrimaryIterator< T >::answer(), ReadData::beginGood(), doc, ReadData::endGood(), ReadData::endPos(), ReadData::mate(), mate_lengths, ReadData::mateLength(), mates, ReadData::name(), names, ReadData::row(), seq_begin_global, seq_beginGood, seq_end_global, seq_endGood, seq_rows, Database::PrimaryIterator< T >::setFromRecno(), ReadData::startPos(), ReadData::strand(), and strands.

Referenced by read_from_db().

00417 {
00418 
00419   Database::PrimaryIterator<ReadData> read_it(doc, "ReadData");
00420 
00421   int ret_read = read_it.setFromRecno(recno);
00422   ReadData* r_test = (ret_read != DB_NOTFOUND) ? read_it.answer() : 0;
00423   assert( r_test );
00424 
00425   seq_begin_global[ buffID ] = r_test->startPos();
00426   seq_end_global[ buffID ] = r_test->endPos() + 1;//Index annoyance...
00427   seq_rows[ buffID ] = r_test->row();
00428   names[ buffID ] = r_test->name();
00429   mates[ buffID ] = r_test->mate();
00430   strands[ buffID ] = r_test->strand();
00431   seq_beginGood[ buffID ] = r_test->beginGood();
00432   seq_endGood[ buffID ] = r_test->endGood() + 1;
00433   mate_lengths[ buffID ] = r_test->mateLength();
00434   
00435 //   cerr<<"Reading seq: "<<endl;
00436 //   cerr<<"recno: "<<recno<<endl;
00437 //   cerr<<"r_test->startPos(): "<<r_test->startPos()<<endl;
00438 //   cerr<<"r_test->endPos(): "<<r_test->endPos()<<endl;
00439 
00440 }

void MAl_Readonly::select_read (  size_t  ID,
bool  status
) 
 

Definition at line 140 of file mal_readonly.cc.

References ID_to_dbID, and selectedReads.

Referenced by StrandsAlgo::start(), ReadListAlgo::start(), and DnpSearchAlgo::start().

00141 {
00142   
00143   assert( ID < ID_to_dbID.size() );
00144   
00145   db_recno_t recno = ID_to_dbID[ ID ];
00146   if ( recno == 0 ) return;
00147 
00148   set<db_recno_t>::iterator pos;
00149   if ( status == true )
00150     selectedReads.insert( recno );
00151   else if ( ( pos = selectedReads.find( recno )) != selectedReads.end() ) {
00152     selectedReads.erase( pos );
00153   }
00154   
00155   
00156 }

Member Data Documentation

size_t MAl_Readonly::buff_size [protected]
 

Definition at line 129 of file mal_readonly.h.

vector<db_recno_t> MAl_Readonly::buffID_to_dbID [protected]
 

Definition at line 154 of file mal_readonly.h.

Referenced by MAl::commit_feat_to_db(), MAl::commit_seq_to_db(), MAl::flush_buffer(), and read_from_db().

vector<db_recno_t> MAl_Readonly::buffID_to_ID [protected]
 

Definition at line 155 of file mal_readonly.h.

Referenced by MAl::flush_buffer(), and read_from_db().

std::vector<std::vector<dnp_struct> > MAl_Readonly::DNPs [protected]
 

Definition at line 138 of file mal_readonly.h.

Referenced by MAl::commit_feat_to_db(), MAl::create_seq(), get_DNP_ID(), get_DNP_type(), MAl::insert_gap(), is_DNP(), read_feat_from_db(), MAl::remove_gap(), MAl::set_DNP(), MAl::set_DNP_ID(), and MAl::set_DNP_type().

TrapperDoc* MAl_Readonly::doc [protected]
 

Definition at line 131 of file mal_readonly.h.

Referenced by MAl::commit_feat_to_db(), MAl::commit_seq_to_db(), read_feat_from_db(), and read_seq_from_db().

std::vector<std::string> MAl_Readonly::headers [protected]
 

Definition at line 140 of file mal_readonly.h.

Referenced by get_header().

vector<size_t> MAl_Readonly::ID_to_buffID [protected]
 

Definition at line 153 of file mal_readonly.h.

Referenced by MAl::create_seq(), MAl::flush_buffer(), get_buffID(), and read_from_db().

vector<db_recno_t> MAl_Readonly::ID_to_dbID [protected]
 

Definition at line 152 of file mal_readonly.h.

Referenced by MAl::create_seq(), read_from_db(), and select_read().

std::vector<size_t> MAl_Readonly::mate_lengths [protected]
 

Definition at line 149 of file mal_readonly.h.

Referenced by MAl::commit_seq_to_db(), and read_seq_from_db().

std::vector<std::string> MAl_Readonly::mates [protected]
 

Definition at line 141 of file mal_readonly.h.

Referenced by MAl::commit_seq_to_db(), and read_seq_from_db().

std::vector<std::string> MAl_Readonly::names [protected]
 

Definition at line 139 of file mal_readonly.h.

Referenced by MAl::commit_seq_to_db(), get_name(), and read_seq_from_db().

size_t MAl_Readonly::num_seq [protected]
 

Definition at line 130 of file mal_readonly.h.

Referenced by MAl::create_seq(), and get_num_seq().

vector<bool> MAl_Readonly::put_in_db [protected]
 

Definition at line 156 of file mal_readonly.h.

Referenced by MAl::flush_buffer(), get_buffID(), read_from_db(), and MAl::~MAl().

std::vector<std::vector<qual_t> > MAl_Readonly::quals [protected]
 

Definition at line 137 of file mal_readonly.h.

Referenced by MAl::commit_feat_to_db(), MAl::create_seq(), get_qual(), MAl::insert_gap(), read_feat_from_db(), MAl::remove_gap(), and MAl::set_qual().

std::set<db_recno_t>& MAl_Readonly::selectedReads [protected]
 

Definition at line 132 of file mal_readonly.h.

Referenced by select_read().

std::vector<size_t> MAl_Readonly::seq_begin_global [protected]
 

Definition at line 145 of file mal_readonly.h.

Referenced by MAl::commit_feat_to_db(), MAl::commit_seq_to_db(), get_seq_begin_global(), read_seq_from_db(), and MAl::set_seq_begin_global().

std::vector<size_t> MAl_Readonly::seq_beginGood [protected]
 

Definition at line 147 of file mal_readonly.h.

Referenced by MAl::commit_seq_to_db(), get_beginGood(), read_seq_from_db(), and MAl::set_beginGood().

std::vector<size_t> MAl_Readonly::seq_end_global [protected]
 

Definition at line 146 of file mal_readonly.h.

Referenced by MAl::commit_feat_to_db(), MAl::commit_seq_to_db(), get_seq_end_global(), read_seq_from_db(), and MAl::set_seq_end_global().

std::vector<size_t> MAl_Readonly::seq_endGood [protected]
 

Definition at line 148 of file mal_readonly.h.

Referenced by MAl::commit_seq_to_db(), get_endGood(), read_seq_from_db(), and MAl::set_endGood().

std::vector<size_t> MAl_Readonly::seq_rows [protected]
 

Definition at line 144 of file mal_readonly.h.

Referenced by MAl::commit_seq_to_db(), get_seq_row(), read_seq_from_db(), and MAl::set_seq_row().

std::vector<std::vector<base_t> > MAl_Readonly::seqs [protected]
 

Definition at line 136 of file mal_readonly.h.

Referenced by MAl::commit_feat_to_db(), MAl::create_seq(), get_base(), get_len(), get_seq(), MAl::insert_gap(), read_feat_from_db(), MAl::remove_gap(), and MAl::set_base().

std::vector<std::string> MAl_Readonly::strands [protected]
 

Definition at line 142 of file mal_readonly.h.

Referenced by MAl::commit_seq_to_db(), get_strand(), and read_seq_from_db().

The documentation for this class was generated from the following files:
Generated on Fri Mar 17 17:44:59 2006 for trapper by  doxygen 1.4.4