QueryManager Class Reference

#include <QueryManager.h>

Collaboration diagram for QueryManager:

[legend]List of all members.

Public Member Functions
	QueryManager (SequenceReader &querySeqs, HashTableGeneric &subjectSeqs, ostream &monitoringStream=cerr)
virtual	~QueryManager ()
void	doQuery (MatchAlgorithm &match, MatchTask &task, int queryStart=1, int queryEnd=-1)
Public Attributes
HashTableGeneric &	subjectTable_
ostream &	monitoringStream_
Protected Attributes
SequenceReader &	queryReader_
MatchPolicy *	policy_
Private Member Functions
	QueryManager (const QueryManager &)
QueryManager &	operator= (const QueryManager &)

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Detailed Description

Definition at line 333 of file QueryManager.h.

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Constructor & Destructor Documentation

QueryManager::QueryManager	(	SequenceReader &	querySeqs,
		HashTableGeneric &	subjectSeqs,
		ostream &	monitoringStream = cerr
	)

Definition at line 387 of file QueryManager.cpp.

References gBaseBits, HashTableGeneric::getBitsPerSymbol(), gResidueBits, MatchPolicyDNADNA::MatchPolicyDNADNA(), and MatchPolicy::subjectTable_.

                                                               :
   queryReader_( querySeqs ), 
   subjectTable_(  subjectSeqs ), 
   monitoringStream_( monitoringStream )
   {
     monitoringStream_ << "constructing QueryManager\n";

     HashTableTranslated* pTransTable
       (dynamic_cast<HashTableTranslated*>(&subjectSeqs));

     if ( pTransTable != NULL )
     {
       if (queryReader_.getBitsPerSymbol()==gResidueBits )
       {
         monitoringStream_ 
         << "Info: running protein query against translated DNA hash table.\n";
         policy_ = new MatchPolicyProteinTranslated(*pTransTable);
       }         
       else if (queryReader_.getBitsPerSymbol()==gBaseBits )
       {
         monitoringStream_ 
         << "Info: running DNA query against translated DNA hash table.\n";
         policy_ = new MatchPolicyDNATranslated(*pTransTable);
       }
       else assert (1==0);
     }
     else // not a translated table
     {
       HashTablePackedProtein* pProteinTable
         (dynamic_cast<HashTablePackedProtein*>(&subjectSeqs));
       if (pProteinTable!=NULL)
       {

         if (queryReader_.getBitsPerSymbol()==gResidueBits)
         {
           monitoringStream_ 
             << "Info: running protein query against protein hash table."
             << endl;
           policy_ = new MatchPolicyProteinProtein(*pProteinTable);
         } // ~if
         else if (queryReader_.getBitsPerSymbol()==gBaseBits)
         {
           monitoringStream_ 
             << "Info: running DNA query against protein hash table."
             << endl;
           policy_ = new MatchPolicyDNAProtein(*pProteinTable);
         } // ~else if
         else assert (1==0);  
       } // ~if  
       else if (subjectTable_.getBitsPerSymbol()==gBaseBits )
       {
         if (queryReader_.getBitsPerSymbol()==gBaseBits)
         {
           monitoringStream_ 
           << "Info: running DNA query against DNA hash table."
           << endl;
           policy_ = new MatchPolicyDNADNA(subjectSeqs);
         } // ~if
         else
         {
           monitoringStream_ 
           << "Error: can't run protein query against DNA hash table!\n";
           throw SSAHAException
             ("Can't run protein query against DNA hash table!");
         } // ~else
         
       } // ~else if

     } // ~else

   } // ~constructor

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QueryManager::~QueryManager

(

)

[virtual]

Definition at line 460 of file QueryManager.cpp.

References monitoringStream_, and policy_.

   {
     monitoringStream_ << "destructing QueryManager\n";
     delete policy_;
   } // ~constructor

QueryManager::QueryManager

(

const QueryManager &

)

[private]

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Member Function Documentation

void QueryManager::doQuery	(	MatchAlgorithm &	match,
		MatchTask &	task,
		int	queryStart = 1,
		int	queryEnd = -1
	)

Definition at line 468 of file QueryManager.cpp.

References SequenceReader::getLastSequenceName(), SequenceReader::getLastSequenceNumber(), HashTableGeneric::getNameReader(), SequenceReader::getNextSequence(), SequenceReader::getSequence(), monitoringStream_, queryReader_, SequenceReader::rewind(), subjectTable_, and wordLength.

Referenced by main(), and processQuery().

  {
    int numBasesInLast(0);
    int wordLength( (*policy_).getWordLength() );

    WordSequence querySeqFwd;

    queryReader_.rewind();

    if ( queryStart == 1 ) 
    {
      numBasesInLast = queryReader_.getNextSequence
                         ( querySeqFwd, wordLength );
    } // ~if 
    else if ( queryStart > 1 ) 
    {
      numBasesInLast = queryReader_.getSequence
      ( querySeqFwd, queryStart, wordLength );
    } // ~else if
    else throw SSAHAException("Invalid query start value!");

    if ( numBasesInLast == -1 )
    {
      monitoringStream_ << "Info: requested sequence start (" << queryStart
      << ") exceeds number of sequences in query database.\n";
      return;
    } // ~if

    do
    {

      string queryName;
      queryReader_.getLastSequenceName( queryName );
      int queryNum = queryReader_.getLastSequenceNumber();
      int queryBases = ( querySeqFwd.size() - 1 )*wordLength 
        + querySeqFwd.getNumBasesInLast();

      MatchStoreImp store
      ( queryName, 
        queryNum, 
        queryBases,  
        subjectTable_.getNameReader() );

      //      cout << "QM: doing " << queryNum << endl;
      (*policy_)( querySeqFwd, store, match );

      store.setup();

      task( store );

      if ( queryReader_.getLastSequenceNumber() == queryEnd ) break;

      // clear the query sequence ready to read in next query
      querySeqFwd.clear();


      // read in next query
      numBasesInLast = queryReader_.getNextSequence
                         ( querySeqFwd, wordLength );
    } // ~while
    while ( numBasesInLast != -1 );

    if (    ( queryReader_.getLastSequenceNumber() < queryEnd  )
         && ( queryEnd != - 1 ) )
    {
      monitoringStream_ << "Info: requested final sequence (" << queryEnd
      << ") exceeded number of\nsequences in query database ("
      << queryReader_.getLastSequenceNumber() << ").\n";
    } // ~if
    
    return;

  } // ~QueryManager::doQuery

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QueryManager& QueryManager::operator=

(

const QueryManager &

)

[private]

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Member Data Documentation

HashTableGeneric& QueryManager::subjectTable_

Definition at line 389 of file QueryManager.h.

Referenced by doQuery().

ostream& QueryManager::monitoringStream_

Definition at line 390 of file QueryManager.h.

Referenced by doQuery(), and ~QueryManager().

SequenceReader& QueryManager::queryReader_ [protected]

Definition at line 397 of file QueryManager.h.

Referenced by doQuery().

MatchPolicy* QueryManager::policy_ [protected]

Definition at line 398 of file QueryManager.h.

Referenced by ~QueryManager().

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The documentation for this class was generated from the following files:

• QueryManager/QueryManager.h
• QueryManager/QueryManager.cpp

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