EnsemblServer/SSAHAWrapper.cpp File Reference

#include "SSAHAWrapper.h"
#include "SequenceReaderFasta.h"
#include "HashTableTranslated.h"
#include "SequenceEncoder.h"
#include <vector>
#include <string>

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Classes
struct	CustomHitStore
class	HashTablePackedCustom
Functions
static HashTableGeneric *	pHashTable (NULL)
const char *	getSubjectName (unsigned int seqNum)
int	loadTable (const char *const tableName)
int	doSearch (const char *const pWords, const int numWords, SSAHAHit **const pHits, int **const pStarts)
int	clearSearch (void)
int	clearTable (void)
Variables
static const int	wordLength = 5
static SequenceEncoderProtein	encoder (wordLength, cerr)
static CustomHitStore	hits
static PackedHitStore	hitBuffer
static vector< int >	hitStarts
static bool	isPacked = false

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Function Documentation

int clearSearch

(

void

)

Definition at line 227 of file SSAHAWrapper.cpp.

References hits.

Referenced by doSearch(), loadTable(), and main().

{
  hits.clear();
  hitStarts.clear();
}

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int clearTable

(

void

)

Definition at line 234 of file SSAHAWrapper.cpp.

References pHashTable.

Referenced by loadTable(), and main().

{
  delete pHashTable;
  pHashTable = NULL;
}

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int doSearch	(	const char *const	pWords,
		const int	numWords,
		SSAHAHit **const	pHits,
		int **const	pStarts
	)

Definition at line 163 of file SSAHAWrapper.cpp.

References clearSearch(), HashTablePackedCustom::convertHits(), SequenceEncoder::encode(), encoder, hitBuffer, hits, SequenceEncoder::linkSeq(), HashTableView< T, SUBCLASS >::matchWord(), pHashTable, HashTablePackedProtein::setQueryProtein(), and SequenceEncoder::unlinkSeq().

Referenced by main().

{
  clearSearch();
  //  SequenceEncoderProtein encoder(wordLength, cerr);
  WordSequence w;

  encoder.linkSeq(w);
  encoder.encode(pWords, numWords*wordLength);
  encoder.unlinkSeq();

  if(w.empty())
  {
    hitStarts.push_back(-1);
    *pHits=NULL;
    *pStarts=&hitStarts[0];
    return -1;
  }


  if (isPacked)
  {
    HashTablePackedCustom* pTable
      = dynamic_cast<HashTablePackedCustom*>(pHashTable);
    assert(pTable!=NULL);
    pTable->setQueryProtein();
    for (WordSequence::iterator i(w.begin());i!=&w.back();i++)
    {
      //    cout << "got: " << printResidue(*i, wordLength) << endl;
      hitBuffer.clear();
      pTable->matchWord( *i, hitBuffer );
      //    pHashTable->convertHits( hitBuffer, hits );
      pTable->convertHits();
      hitStarts.push_back(hits.size());
    }
  } // ~for
  else
  {
    HashTableFred* pTable
      = dynamic_cast<HashTableFred*>(pHashTable);
    assert(pTable!=NULL);
    //    int n(hits.size());
    for (WordSequence::iterator i(w.begin());i!=&w.back();i++)
    {
      pTable->matchWord( *i, hits );
    }
    hitStarts.push_back(hits.size());
  }


  //  hits.push_back();
  //  hits.back().seqNum=1103; hits.back().seqPos=-1103;
  //  hitStarts.push_back(1);
  hitStarts.push_back(-1);
  *pHits=&hits[0];
  *pStarts=&hitStarts[0];
  return 0;
}

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const char* getSubjectName

(

unsigned int

seqNum

)

Definition at line 134 of file SSAHAWrapper.cpp.

References HashTableGeneric::getSequenceName(), and pHashTable.

Referenced by main().

{
  return pHashTable->getSequenceName( seqNum );
} // ~const char* getSubjectName( unsigned int seqNum )

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int loadTable

(

const char *const

tableName

)

Definition at line 141 of file SSAHAWrapper.cpp.

References clearSearch(), clearTable(), HashTableGeneric::getWordLength(), HashTablePackedCustom::HashTablePackedCustom(), HashTableGeneric::loadHashTable(), pHashTable, and HashTableGeneric::setMaxNumHits().

Referenced by main().

{
  clearSearch();
  clearTable();

  if (isPacked)
  {
    pHashTable = new HashTablePackedCustom( cerr, (string)tableName);
  }
  else
  {
    pHashTable = new HashTableFred( cerr, (string)tableName);
  }

  pHashTable->loadHashTable(); 
  // will throw exception if fails, eg if trying to load wrong table
  assert(pHashTable->getWordLength()==wordLength);
  pHashTable->setMaxNumHits( 100000000 );
}

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static HashTableGeneric* pHashTable

(

NULL

)

[static]

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Variable Documentation

SequenceEncoderProtein encoder(wordLength, cerr) [static]

Referenced by doSearch(), fillSequenceReaderMulti(), findSequenceReader(), and main().

PackedHitStore hitBuffer [static]

Definition at line 68 of file SSAHAWrapper.cpp.

Referenced by HashTablePackedCustom::convertHits(), and doSearch().

CustomHitStore hits [static]

Definition at line 66 of file SSAHAWrapper.cpp.

Referenced by clearSearch(), HashTablePackedCustom::convertHits(), doSearch(), main(), HashTablePacked::matchSequenceRepeated(), and HashTable::matchSequenceRepeated().

vector<int> hitStarts [static]

Definition at line 69 of file SSAHAWrapper.cpp.

bool isPacked = false [static]

Definition at line 70 of file SSAHAWrapper.cpp.

const int wordLength = 5 [static]

Definition at line 64 of file SSAHAWrapper.cpp.

Referenced by QueryManager::doQuery(), main(), MatchAlgorithm::operator()(), and WordSequenceShifted::WordSequenceShifted().

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