HashTableFactory Class Reference

#include <HashTableGeneric.h>

List of all members.

Public Member Functions
	HashTableFactory (ostream &monStream=cerr)
void	createHashTable (HashTableGeneric &ht, SequenceReader &sequenceReader, int wordLength, int maxNumHits, int stepLength=0)
HashTableGeneric *	loadHashTable (const string &name, SourceReaderIndex *pReader=NULL)
void	loadHashTable (HashTableGeneric &ht, SourceReaderIndex *pReader=NULL)
void	saveHashTable (HashTableGeneric &ht)
Public Attributes
ostream &	monitoringStream_

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Detailed Description

Definition at line 422 of file HashTableGeneric.h.

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Constructor & Destructor Documentation

HashTableFactory::HashTableFactory

(

ostream &

monStream = cerr

)

[inline]

Definition at line 425 of file HashTableGeneric.h.

                                              : monitoringStream_(monStream)
  {}

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Member Function Documentation

void HashTableFactory::createHashTable	(	HashTableGeneric &	ht,
		SequenceReader &	sequenceReader,
		int	wordLength,
		int	maxNumHits,
		int	stepLength = 0
	)			[inline]

Definition at line 433 of file HashTableGeneric.h.

References HashTableGeneric::createHashTable().

Referenced by main(), and processQuery().

  {
    ht.createHashTable
      ( sequenceReader, wordLength, maxNumHits, stepLength );
  }

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HashTableGeneric * HashTableFactory::loadHashTable	(	const string &	name,
		SourceReaderIndex *	pReader = NULL
	)

Definition at line 485 of file HashTableGeneric.cpp.

References g32BitPacked, g32BitPackedProtein, gStandard, gTranslated, HashTableGeneric::isInitialized(), and monitoringStream_.

Referenced by generateHashTable(), main(), and processQuery().

  {

    monitoringStream_ << "loading hash table from file ...\n";

    ifstream nameFile( (name+(string)".name").c_str() );
    
    if ( nameFile.fail() )
    {
      monitoringStream_ << "Error: failed to open " 
                        << name << ".name, aborting load." << endl;
      throw SSAHAException("Could not open .name file ");
    } // ~if

    char firstChar = nameFile.peek();
    string temp;
    temp += firstChar;
    
    nameFile.close();

    HitListFormatType hitListFormat((HitListFormatType)atoi(temp.c_str()));

    HashTableGeneric* pTable(NULL);

    if (hitListFormat==gStandard)
    {
      monitoringStream_ << "... creating standard format hash table\n";
      pTable = new HashTable(monitoringStream_,name);
    } // ~if
    else if (hitListFormat==g32BitPacked)
    {
      monitoringStream_ << "... creating 32 bit packed format hash table\n";
      pTable = new HashTablePacked(monitoringStream_,name);
    } // ~else if
    else if (hitListFormat==g32BitPackedProtein)
    {
      monitoringStream_ 
        << "... creating 32 bit packed format protein hash table\n";
      pTable = new HashTablePackedProtein(monitoringStream_,name);
    } // ~else if
    else if (hitListFormat==gTranslated)
    {
      monitoringStream_ << "... creating translated format hash table\n";
      pTable = new HashTableTranslated(monitoringStream_,name);
    }
    else
    {
      monitoringStream_ 
        << "Error: type of hash table (" << hitListFormat 
        << " not recognised.\n";
      throw SSAHAException("Could not recognise hash table type");
    } // ~else

    assert (pTable!=NULL);
    
    loadHashTable(*pTable, pReader);

    assert (pTable->isInitialized());

    return pTable;

  }

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void HashTableFactory::loadHashTable	(	HashTableGeneric &	ht,
		SourceReaderIndex *	pReader = NULL
	)			[inline]

Definition at line 472 of file HashTableGeneric.h.

References HashTableGeneric::loadHashTable().

  {
    ht.loadHashTable(pReader);
  }

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void HashTableFactory::saveHashTable

(

HashTableGeneric &

ht

)

[inline]

Definition at line 485 of file HashTableGeneric.h.

References HashTableGeneric::saveHashTable().

Referenced by main(), and processQuery().

  {
    ht.saveHashTable();
  }

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Member Data Documentation

ostream& HashTableFactory::monitoringStream_

Definition at line 491 of file HashTableGeneric.h.

Referenced by HashTableGeneric::loadHashTable(), and loadHashTable().

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

• HashTable/HashTableGeneric.h
• HashTable/HashTableGeneric.cpp

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