ngsview: trapperdoc.cpp Source File

00001 /*******************************************************************************
00002  *                                                                             *
00003  *   Copyright (C) 2003  Erik Sjolund,  (<html>Erik Sj&ouml;lund</html>)       *
00004  *                       Center for Genomics and Bioinformatics,               *
00005  *                       Karolinska Institutet,                                *
00006  *                       Stockholm,                                            *
00007  *                       Sweden                                                *
00008  *                                                                             *
00009  *  Author: Erik Sjolund                                                       *
00010  *  Email: erik.sjolund@adivo.se                                               *
00011  *                                                                             *
00012  *******************************************************************************
00013  */
00014 // qt classes
00015 #include <qdir.h>
00016 #include <qfileinfo.h>
00017 #include <qwidget.h>
00018 #include <qmsgbox.h>
00019 #include <qfiledialog.h>
00020 #include <qdom.h>
00021 #include <qxml.h>
00022 // stl
00023 #include <iostream>
00024 #include <list>
00025 #include <vector>
00026 #include <string>
00027 #include <ostream>
00028 // application specific
00029 #include "trapperdoc.h"
00030 #include "trapper.h"
00031 #include "trapperview.h"
00032 #include "generaldata.h"
00033 #include "algo.h"
00034 #include "trdb.h"
00035 #include "featuredata.h"
00036 #include "readdata.h"
00037 #include "generalmaker.h"
00038 #include "chromatparser.h"
00039 #include "mateparser.h"
00040 #include "tcparser.h"
00041 #include "phdparser.h"
00042 using namespace std;
00043 
00044 TrapperDoc::TrapperDoc(DbEnv * dbenv_): dbenv( dbenv_ )
00045 {
00046 //     qDebug("in TrapperDoc::TrapperDoc()");
00047     pViewList = new QList<TrapperView>;
00048 //     pViewList->setAutoDelete(false);
00049     pViewList->setAutoDelete(true);
00050     pAlgoList = new QList<Algo>;
00051     pAlgoList->setAutoDelete(false);
00052     setModified(true );
00053 }
00054 
00055 TrapperDoc::~TrapperDoc()
00056 {
00057 //   cerr<<"closing doc"<<endl;
00058   delete pViewList;
00059   delete pAlgoList;
00060   closeDbs();
00061 }
00062 
00063 void TrapperDoc::addView(TrapperView *view)
00064 {
00065     pViewList->append(view);
00066     changedViewList();
00067 }
00068 
00069 void TrapperDoc::addAlgorithm(Algo *algo)
00070 {
00071     pAlgoList->append(algo);
00072     changedAlgoList();
00073 }
00074 
00075 void TrapperDoc::removeView(TrapperView *view)
00076 {
00077     pViewList->remove
00078     (view);
00079     if(!pViewList->isEmpty() || !pAlgoList->isEmpty() )
00080         changedViewList();
00081     else
00082         deleteContents();
00083 }
00084 
00085 void TrapperDoc::removeAlgorithm(Algo *algo)
00086 {
00087     pAlgoList->remove
00088     (algo);
00089     if(!pViewList->isEmpty() || !pAlgoList->isEmpty() )
00090         changedAlgoList();
00091     else
00092         deleteContents();
00093 }
00094 
00095 void TrapperDoc::changedViewList()
00096 {
00097 
00098     TrapperView *w;
00099     if((int)pViewList->count() == 1)
00100     {
00101         w=pViewList->first();
00102         QString mode = w->mode();
00103         w->setCaption(QString(m_title+" mode=%2").arg(mode));
00104     }
00105     else
00106     {
00107         int i;
00108         for( i=1,w=pViewList->first(); w!=0; i++, w=pViewList->next())
00109         {
00110             QString mode = w->mode();
00111             w->setCaption(QString(m_title+" :%1 mode=%2").arg(i).arg(mode));
00112         }
00113     }
00114 }
00115 
00116 void TrapperDoc::changedAlgoList()
00117 {
00118 }
00119 
00120 bool TrapperDoc::isLastView()
00121 {
00122     return ((int) pViewList->count() == 1);
00123 }
00124 
00125 void TrapperDoc::updateAllViews(TrapperView *sender)
00126 {
00127     TrapperView *w;
00128     for(w=pViewList->first(); w!=0; w=pViewList->next())
00129     {
00130         w->update(sender);
00131     }
00132 }
00133 
00134 void TrapperDoc::setPathName(const QString &name)
00135 {
00136     m_contigDir=name;
00137     m_title=QFileInfo(name).fileName();
00138 }
00139 
00140 const QString& TrapperDoc::pathName() const
00141 {
00142     return m_contigDir;
00143 }
00144 
00145 void TrapperDoc::setTitle(const QString &title)
00146 {
00147     m_title=title;
00148 }
00149 
00150 const QString &TrapperDoc::title() const
00151 {
00152     return m_title;
00153 }
00154 
00155 void TrapperDoc::closeDocument()
00156 {
00157   cerr<<"closeDocument()"<<endl;
00158   TrapperView *w;
00159   if(!isLastView()) {
00160     for(w=pViewList->first(); w!=0; w=pViewList->next()) {
00161       if(!w->close())
00162         break;
00163     }
00164   }
00165   if(isLastView()) {
00166     w = pViewList->first();
00167     w->close();
00168   }
00169 }
00170 
00171 bool TrapperDoc::newDocument()
00172 {
00173     /////////////////////////////////////////////////
00174     // TODO: Add your document initialization code here
00175     /////////////////////////////////////////////////
00176     modified=false;
00177     return true;
00178 }
00179 
00180 bool TrapperDoc::openDocument(const QString &dirname )
00181 {
00182 //   cerr<<"openDocument() "<<endl;
00183   m_contigDir=dirname;
00184   QDir dir( m_contigDir );
00185   
00186   if ( !dir.exists() ) {
00187     QDir dir2;
00188     if ( !dir2.mkdir( m_contigDir, true ) ) {
00189       // oops, still doesn't exist
00190       cerr << "creating new dir failed, dir name=" << m_contigDir << endl;
00191       exit(1);
00192       
00193       
00194     }
00195   }
00196   /////////////////////////////////////////////////
00197   // TODO: Add your document opening code here
00198   /////////////////////////////////////////////////
00199   modified=false;
00200   m_title=dirname;
00201   
00202   openDbs();
00203   return true;
00204 }
00205 
00206 bool TrapperDoc::saveDocument(const QString &filename, const char * /* format */)
00207 {
00208     /* we are using the berkeley db so changes are automatically changed in the files
00209        after the commit of the transaction.
00210        Here we might instead have some change of m_contigdir, to move the contig dir to
00211        another name to reflect the change of a "sandbox" contig to a regular contig. 
00212     */
00213     return false;
00214 
00215     /////////////////////////////////////////////////
00216     // TODO: Add your document saving code here
00217     /////////////////////////////////////////////////
00218 
00219     modified=false;
00220     m_contigDir=filename;
00221     m_title=filename;
00222     return true;
00223 }
00224 
00225 void TrapperDoc::deleteContents()
00226 {
00227     /////////////////////////////////////////////////
00228     // TODO: Add implementation to delete the document contents
00229     /////////////////////////////////////////////////
00230 
00231 }
00232 
00233 bool TrapperDoc::canCloseFrame(TrapperView* pFrame)
00234 {
00235     if(!isLastView())
00236         return true;
00237 
00238     bool ret=false;
00239     if(isModified())
00240     {
00241         QString saveName;
00242         switch(QMessageBox::information(pFrame, title(), tr("The current file has been modified.\n"
00243                                         "Do you want to save it?"),QMessageBox::Yes, QMessageBox::No, QMessageBox::Cancel ))
00244         {
00245         case QMessageBox::Yes:
00246             if(title().contains(tr("Untitled")))
00247             {
00248                 saveName=QFileDialog::getSaveFileName(0, 0, pFrame);
00249                 if(saveName.isEmpty())
00250                     return false;
00251             }
00252             else
00253                 saveName=pathName();
00254 
00255             if(!saveDocument(saveName))
00256             {
00257                 switch(QMessageBox::critical(pFrame, tr("I/O Error !"), tr("Could not save the current document !\n"
00258                                              "Close anyway ?"),QMessageBox::Yes ,QMessageBox::No))
00259 
00260                 {
00261                 case QMessageBox::Yes:
00262                     ret=true;
00263                 case QMessageBox::No:
00264                     ret=false;
00265                 }
00266             }
00267             else
00268                 ret=true;
00269             break;
00270         case QMessageBox::No:
00271             ret=true;
00272             break;
00273         case QMessageBox::Cancel:
00274         default:
00275             ret=false;
00276             break;
00277         }
00278     }
00279     else
00280         ret=true;
00281 
00282     return ret;
00283 }
00284 
00285 void TrapperDoc::saveExport(ostream& stream)
00286 {
00287 
00288   //Ugly fix for strange behaviour...
00289   int offset(-1);
00290   if ( pathName()[pathName().length() -1] == '/' ) {
00291     --offset;
00292   }
00293   
00294   stream<<"<contig name=\""<<pathName().section('/', offset)<<"\">\n";
00295   
00296   Database::PrimaryIterator<ReadData> iter( this, "ReadData" );
00297 
00298   if ( iter.first() == 0 ) {
00299     do {
00300       //ReadData
00301       iter.answer()->writeXml(stream);
00302       //FeatureData
00303       
00304       list<string> alist = GeneralMaker::listRegistered();
00305       for ( list<string>::iterator  it = alist.begin(); it != alist.end(); ++it ) {
00306         if ( *it == "ReadData") {
00307           continue;
00308         }
00309         Database::SecondaryIterator<FeatureData> f_it( "readRecno", this, *it );
00310         
00311         f_it.key()->setReadRecno( iter.answer()->getRecno() );
00312         
00313         if ( f_it.set() == 0 ) {
00314           do {
00315             f_it.answer()->writeXml(stream);
00316             
00317           }while(f_it.nextdup() == 0);
00318         }
00319       }
00320       
00321       //End ReadData
00322       stream<<"</ReadData>\n";
00323         
00324     }while( iter.next() == 0 );
00325     
00326     
00327   }
00328   
00329   stream<<"</contig>\n";
00330   
00331 }
00332 
00333 bool TrapperDoc::import(QDomElement & elem1)
00334 {
00335   QDomNode node2 = elem1.firstChild();
00336   
00337   while ( !node2.isNull() )
00338     {
00339       if ( node2.isElement() )
00340         {
00341           QString generalDataName = node2.nodeName();
00342           QDomElement elem2 = node2.toElement();
00343           
00344           Database::Creator<GeneralData> creator( this, generalDataName.ascii() );
00345           
00346           QDomNode node3 = elem2.firstChild();
00347           
00348           while ( !node3.isNull() )
00349             {
00350               if ( node3.isElement() && node3.nodeName() == "record" )
00351                 {
00352                   QDomElement elem3 = node3.toElement();
00353                   
00354                   creator.data()->readDom( elem3 );
00355                   creator.create( true );
00356                 }
00357               node3 = node3.nextSibling();
00358             }
00359         }
00360       node2 = node2.nextSibling();
00361     }
00362   return true;
00363 }
00364 
00365 void TrapperDoc::importChromat(const QString& dirname)
00366 {
00367   //Get all readnames
00368   
00369   vector<string> names = all_readnames();
00370   
00371   //Parse files
00372 
00373   for( size_t i = 0; i < names.size(); i++ ) {
00374 
00375 
00376     vector<TrapperVector<Q_UINT32> > chromat_array;
00377     ChromatParser handler;
00378     handler.set_result_array( &chromat_array );
00379     QFile xmlFile( dirname + '/' + names[i] + ".xml" );
00380     QXmlInputSource source( &xmlFile );
00381     QXmlSimpleReader reader;
00382     reader.setContentHandler( &handler );
00383     if ( !reader.parse( source ) ) {
00384       cerr<<"Error, couldn't find chromatogram for "<<names[i]<<endl;
00385       continue;
00386     }
00387     //First, find recno of read
00388 //     Database::SecondaryIterator<ReadData> name_it( "name", this, "ReadData" );
00389 //     name_it.key()->setName( names[i] );
00390 //     if ( name_it.set() != 0 ) {
00391 //       cerr<<"Error, couldn't find "<<names[i]<<" in db"<<endl;
00392 //       continue;
00393 //     }
00394 
00395     Database::SecondaryIterator<ReadMetaData> name_it( "name", this, "ReadMetaData" );
00396     name_it.key()->setName( names[i] );
00397     if ( name_it.set() != 0 ) {
00398       cerr<<"Error, couldn't find "<<names[i]<<" in db"<<endl;
00399       continue;
00400     }
00401     
00402 
00403     //Second, find corresponding chromat feature data
00404     Database::SecondaryIterator<ChromatData>* chr_it = 
00405       new Database::SecondaryIterator<ChromatData>( "readRecno", this, "ChromatData" );
00406     
00407     chr_it->key()->setReadRecno( name_it.answer()->readRecno() );
00408     
00409     if ( chr_it->set() != 0 ) {
00410       cerr<<"Error, couldn't find recno "<<name_it.answer()->readRecno()<<" of read "<<names[i]<<endl;
00411       delete chr_it;
00412       continue;
00413     }
00414 
00415     //Create new data
00416     Database::Creator<ChromatData> creator( this, "ChromatData" );
00417     
00418     creator.data()->copy(chr_it->answer());
00419 
00420     
00421     creator.data()->cagt_vec.clear();
00422     if ( name_it.answer()->strand() == "C" ) {
00423 
00424       creator.data()->cagt_vec.push_back(TrapperVector<Q_UINT32>());
00425       creator.data()->cagt_vec.push_back(TrapperVector<Q_UINT32>());
00426       creator.data()->cagt_vec.push_back(TrapperVector<Q_UINT32>());
00427       creator.data()->cagt_vec.push_back(TrapperVector<Q_UINT32>());
00428 
00429       //Revcomp, must reverse the chromat and switch curves A->T, G->C
00430 
00431       creator.data()->cagt_vec[0].stlVector().clear();
00432       creator.data()->cagt_vec[0].stlVector().insert(creator.data()->cagt_vec[0].stlVector().begin(),
00433                                          chromat_array[2].stlVector().rbegin(), chromat_array[2].stlVector().rend());
00434       creator.data()->cagt_vec[1].stlVector().clear();
00435       creator.data()->cagt_vec[1].stlVector().insert(creator.data()->cagt_vec[1].stlVector().begin(),
00436                                          chromat_array[3].stlVector().rbegin(), chromat_array[3].stlVector().rend());
00437       creator.data()->cagt_vec[2].stlVector().clear();
00438       creator.data()->cagt_vec[2].stlVector().insert(creator.data()->cagt_vec[2].stlVector().begin(),
00439                                          chromat_array[0].stlVector().rbegin(), chromat_array[0].stlVector().rend());
00440       creator.data()->cagt_vec[3].stlVector().clear();
00441       creator.data()->cagt_vec[3].stlVector().insert(creator.data()->cagt_vec[3].stlVector().begin(),
00442                                          chromat_array[1].stlVector().rbegin(), chromat_array[1].stlVector().rend());
00443       
00444     }
00445     else {
00446     
00447       creator.data()->cagt_vec = chromat_array;
00448     }
00449     
00450     delete chr_it;
00451     
00452     creator.create(true);
00453   }
00454 
00455 
00456 }
00457 
00458 void TrapperDoc::importPhd(const QString& dirname)
00459 {
00460   //Get all readnames
00461   
00462   vector<string> names = all_readnames();
00463   
00464   //Parse files
00465 
00466   for( size_t i = 0; i < names.size(); i++ ) {
00467 
00468     TrapperVector<Q_UINT32> phd_array;
00469 
00470     PhdParser parser(dirname + '/' + names[i] + ".phd.1");
00471     phd_array = parser.parse();
00472     
00473     if ( phd_array.size() == 0 ) {
00474       cerr<<"Error, couldn't find phd file for "<<names[i]<<endl;
00475       continue;
00476     }
00477     //First, find recno of read
00478 //     Database::SecondaryIterator<ReadData> name_it( "name", this, "ReadData" );
00479 //     name_it.key()->setName( names[i] );
00480 //     if ( name_it.set() != 0 ) {
00481 //       cerr<<"Error, couldn't find "<<names[i]<<" in db"<<endl;
00482 //       continue;
00483 //     }
00484 
00485     Database::SecondaryIterator<ReadMetaData> name_it( "name", this, "ReadMetaData" );
00486     name_it.key()->setName( names[i] );
00487     if ( name_it.set() != 0 ) {
00488       cerr<<"Error, couldn't find "<<names[i]<<" in db"<<endl;
00489       continue;
00490     }
00491     //Second, find corresponding chromat feature data
00492     Database::SecondaryIterator<ChromatData>* chr_it = 
00493       new Database::SecondaryIterator<ChromatData>( "readRecno", this, "ChromatData" );
00494     
00495     chr_it->key()->setReadRecno( name_it.answer()->readRecno() );
00496     
00497     if ( chr_it->set() != 0 ) {
00498       cerr<<"Error, couldn't find recno "<<name_it.answer()->readRecno()<<" of read "<<names[i]<<endl;
00499       delete chr_it;
00500       continue;
00501     }
00502     if ( chr_it->answer()->cagt_vec[0].stlVector().size() == 0 ) {
00503       cerr<<"Chromat file for "<<names[i]<<" not imported, skipping phd file"<<endl;
00504       delete chr_it;
00505       continue;
00506     }
00507 
00508     //Create new data
00509     Database::Creator<ChromatData> creator( this, "ChromatData" );
00510 
00511     creator.data()->copy(chr_it->answer());
00512 
00513     if ( name_it.answer()->strand() == "C" ) {
00514       creator.data()->phd_vec.stlVector().clear();
00515       creator.data()->phd_vec.stlVector().insert(creator.data()->phd_vec.stlVector().begin(),
00516                                                  phd_array.stlVector().rbegin(), phd_array.stlVector().rend());
00517       for( size_t i = 0; i < creator.data()->phd_vec.stlVector().size(); i++ ) {
00518         creator.data()->phd_vec.stlVector()[i] = creator.data()->cagt_vec[0].stlVector().size() - 1 - creator.data()->phd_vec.stlVector()[i];
00519       }
00520     }
00521     else {
00522       
00523       creator.data()->phd_vec = phd_array;
00524     }
00525     
00526 
00527     delete chr_it;
00528 
00529     //TEMPORARY FIX OF THE GAP PROBLEM!!!
00530     Database::SecondaryIterator<DnaStrData>* dna_it = 
00531       new Database::SecondaryIterator<DnaStrData>( "readRecno", this, "DnaStrData" );
00532     dna_it->key()->setReadRecno( name_it.answer()->readRecno() );
00533     
00534     if ( dna_it->set() != 0 ) {
00535       cerr<<"Error, couldn't find recno "<<name_it.answer()->readRecno()<<" of read "<<names[i]<<endl;
00536       delete dna_it;
00537       continue;
00538     }
00539     creator.data()->gap_vec.stlVector().clear();
00540     size_t numgap(0);
00541     for( size_t i = 0; i < dna_it->answer()->dnaVector.size(); i++ ) {
00542       if (dna_it->answer()->dnaVector.stlVector()[i] == '*' ) {
00543         numgap++;
00544       }
00545       creator.data()->gap_vec.stlVector().push_back(numgap);
00546     }
00547 
00548     
00549     assert( creator.data()->gap_vec.stlVector().size() == static_cast<size_t>(creator.data()->endPos() + 1) );
00550     delete dna_it;
00551     
00552     //END FIX!!!
00553     
00554     creator.create(true);
00555     
00556   }
00557   
00558 
00559 }
00560 
00561 void TrapperDoc::importMates(const QString& filename)
00562 {
00563   //Get all readnames
00564   
00565 //   vector<string> names = all_readnames();
00566   
00567   //Parse file
00568   MateParser parser;
00569   parser.set_file(filename);
00570   
00571   string read_name, mate_name;
00572   size_t mate_length;
00573 
00574   while( parser.parse_line( read_name, mate_name, mate_length ) ) {
00575 
00576 
00577     //For each read:
00578     
00579     //Add mate data
00580     //NB, assumes that the same read name is present only once in each contig, might need to fix this
00581 
00582 
00583     Database::Creator<ReadMetaData> creator( this, "ReadMetaData" );
00584     
00585     //First, find recno of read with name read_name
00586 //     Database::SecondaryIterator<ReadData>* name_it =
00587 //       new Database::SecondaryIterator<ReadData>( "name", this, "ReadData" );
00588 //     name_it->key()->setName( read_name );
00589 //     if ( name_it->set() != 0 ) {
00590 //       delete name_it;
00591 //       continue;
00592 //     }
00593     Database::SecondaryIterator<ReadMetaData>* name_it =
00594       new Database::SecondaryIterator<ReadMetaData>( "name", this, "ReadMetaData" );
00595     name_it->key()->setName( read_name );
00596     if ( name_it->set() != 0 ) {
00597       delete name_it;
00598       continue;
00599     }
00600     
00601     creator.data()->copy( name_it->answer() );
00602 
00603     creator.data()->setMate( mate_name );
00604     creator.data()->setMateLength( mate_length );
00605     
00606     
00607     delete name_it;
00608     
00609     creator.create(true);
00610     
00611     //Same for mate
00612       
00613     //First, find recno of read with name mate_name
00614 //     name_it = new Database::SecondaryIterator<ReadData>( "name", this, "ReadData" );
00615 //     name_it->key()->setName( mate_name );
00616 //     if ( name_it->set() != 0 ) {
00617 //       delete name_it;
00618 //       continue;
00619 //     }
00620     name_it = new Database::SecondaryIterator<ReadMetaData>( "name", this, "ReadMetaData" );
00621     name_it->key()->setName( read_name );
00622     if ( name_it->set() != 0 ) {
00623       delete name_it;
00624       continue;
00625     }
00626     
00627 
00628     creator.data()->copy( name_it->answer() );
00629     
00630     creator.data()->setMate( read_name );
00631     creator.data()->setMateLength( mate_length );
00632     
00633     
00634     delete name_it;
00635     
00636     creator.create(true);
00637     
00638   }
00639   
00640 }
00641 
00642 void TrapperDoc::importTimeCourse(const QString& filename)
00643 {
00644   //Get all readnames
00645   
00646 //   vector<string> names = all_readnames();
00647   
00648   //Parse file
00649   TcParser parser;
00650   parser.set_file(filename);
00651   
00652   string read_name;
00653   vector<double> time_course;
00654 
00655   while( parser.parse_line( read_name, time_course ) ) {
00656 
00657 
00658     //For each read:
00659     
00660     //Add tc data
00661     //NB, assumes that the same read name is present only once in each contig, might need to fix this
00662 
00663 
00664     Database::Creator<ReadMetaData> creator( this, "ReadMetaData" );
00665     
00666     //First, find recno of read with name read_name
00667     Database::SecondaryIterator<ReadMetaData>* name_it =
00668       new Database::SecondaryIterator<ReadMetaData>( "name", this, "ReadMetaData" );
00669     name_it->key()->setName( read_name );
00670     if ( name_it->set() != 0 ) {
00671       time_course.clear();
00672       delete name_it;
00673       continue;
00674     }
00675     
00676     creator.data()->copy( name_it->answer() );
00677     
00678     creator.data()->tc_vec.stlVector() = time_course;
00679 //     cerr<<"\nName: "<<read_name<<endl;
00680 //     for( size_t i = 0; i < creator.data()->tc_vec.stlVector().size(); i++ ) {
00681 //       cerr<<creator.data()->tc_vec.stlVector()[i]<<" ";
00682 //     }
00683 //     cerr<<endl;
00684     delete name_it;
00685 //     for( size_t i = 0; i < creator.data()->tc_vec.stlVector().size(); i++ ) {
00686 //       cerr<<creator.data()->tc_vec.stlVector()[i]<<" ";
00687 //     }
00688 //     cerr<<endl;
00689     
00690     creator.create(true);
00691     time_course.clear();
00692   }
00693   
00694 }
00695 
00696 
00697 vector<string> TrapperDoc::all_readnames()
00698 {
00699   vector<string> names;
00700 
00701   Database::SecondaryIterator<ReadMetaData> name_it( "name", this, "ReadMetaData" );
00702   assert(name_it.first() == 0);
00703   string name;
00704   
00705   do {
00706     name = name_it.answer()->name().c_str();
00707     names.push_back(name);//Have to use c_str() due to some straaange bug...
00708   }while( name_it.next() == 0 );
00709   
00710   return names;
00711   
00712 }
00713 
00714 
00715 void TrapperDoc::openDbs()
00716 {
00717 
00718   list<string> alist = GeneralMaker::listRegistered();
00719 
00720   for (  list<string>::iterator  it = alist.begin(); it != alist.end(); ++it )
00721     {
00722       GeneralData * data = GeneralMaker::newData( *it );
00723       if ( data )
00724         {
00725           QString directoryName(  m_contigDir );
00726           directoryName += "/";
00727           directoryName += it->c_str() ;
00728           
00729           QDir dir;
00730           dir.mkdir( directoryName , true );
00731           
00732           TrDb * trdb = new TrDb( dbenv, directoryName.ascii() , data->getIndexMap() );
00733           trDbMap.insert( make_pair( it->c_str(), trdb ) );
00734           
00735 //           cerr << "trDbMap.insert( make_pair( it->c_str(), trdb ) ) ******* "
00736 //                << it->c_str() << " ***************** "
00737 //                << directoryName.ascii() << endl;
00738           
00739           delete data;
00740           trdb->open();
00741 
00742 //           cerr<<"trdb->primaryDb(): "<<trdb->primaryDb()<<endl;
00743         }
00744     }
00745 
00746 }
00747 
00748 TrDb * TrapperDoc::findTrDb( string generalDataName )
00749 {
00750     TrDb * trdb = NULL;
00751     TrDbMap::iterator it;
00752     it = trDbMap.find( generalDataName );
00753     if (it != trDbMap.end())
00754     {
00755         trdb = it->second;
00756     }
00757     else
00758     {
00759         cerr << "TrDb for generalData type=\""
00760         << generalDataName << "\" and contig=\""
00761         << m_contigDir << "\" not found" << endl;
00762     }
00763     return trdb;
00764 }
00765 
00766 void TrapperDoc::closeDbs()
00767 {
00768 
00769   TrDbMap::iterator it;
00770   it = trDbMap.begin();
00771 
00772   while (it != trDbMap.end()) {
00773     Q_CHECK_PTR( it->second );
00774     it->second->close();
00775     delete it->second;
00776     ++it;
00777   }
00778   trDbMap.clear();
00779 }
00780 
00781 QString TrapperDoc::getStatistics()
00782 {
00783     QString res;
00784     TrDbMap::iterator it;
00785     it = trDbMap.begin();
00786     while (it != trDbMap.end())
00787     {
00788         Q_CHECK_PTR( it->second );
00789         res += it->second->statistics();
00790         ++it;
00791     }
00792     return res;
00793 }