Global/GlobalDefinitions.h File Reference

#include <unistd.h>
#include <vector>
#include <string>
#include <iostream>
#include <fstream>
#include <map>
#include <utility>
#include <sys/types.h>
#include <stdio.h>
#include <sys/file.h>
#include <sys/mman.h>
#include <sys/stat.h>
#include <errno.h>

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Namespaces
namespace	std
Classes
class	WordSequence
struct	PositionInDatabase
struct	HitInfo
class	HitListVector
class	MachineInfo
class	SSAHAException
class	ofstreamSSAHA
class	ifstreamSSAHA
class	NullBuffer
class	PrintFromWord
class	printBase
class	printResidue
class	MakeIntoWord
class	Allocator< T >
class	AllocatorLocal< T >
Defines
#define	DEBUG_L3(X)
#define	DEBUG_L2(X)
#define	DEBUG_L1(X)
Typedefs
typedef unsigned int	Word
typedef unsigned char	uchar
typedef unsigned short	ushort
typedef WordSequence::iterator	WordSequenceIterator
typedef WordSequence::reverse_iterator	WordSequenceReverseIterator
typedef unsigned int	SequenceNumber
typedef int	SequenceOffset
typedef HitListVector	HitList
typedef printBase	printWord
Enumerations
enum	{   gBaseBits = 2, gResidueBits = 5, gBasesPerCodon = 3, gCodonBits = gBaseBits*gBasesPerCodon,   gBitsPerWord = 8*sizeof(Word), gMaxBasesPerWord = gBitsPerWord / gBaseBits, gNumReadingFrames = 3, gNumDirections = 2,   gNumCodonEncodings = 22 }
enum	SourceDataType { gDNAData = 0, gProteinData = 1, gUnknownData = 2 }
enum	HitListFormatType {   gStandard = 0, g32BitPacked = 1, g32BitPackedProtein = 2, gTranslated = 3,   gHybrid = 4, gNotSpecified = 5 }
Functions
char *	getTimeNow (void)
Word	reverseComplement (Word word, int wordLength)
void	reverseComplement (const WordSequence &seq, WordSequence &revComp, int wordLength)
void	shiftSequence (WordSequence &sequence, int bitsPerSymbol, int wordLength, int i=1)
void	shiftSequenceDNA (WordSequence &sequence, int wordLength, int i=1)
void	shiftSequenceProtein (WordSequence &sequence, int wordLength, int i=1)
void	loadFromFile (const string &fileName, const char *buffer, const unsigned long numBytes, ostream &monitoringStream_=cerr)
void	saveToFile (const string &fileName, const char *buffer, const unsigned long numBytes, ostream &monitoringStream_=cerr)
Variables
static const char	gBaseNames [] = "ACGT"
static const char	gResidueNames [] = "*ACDEFGHIKLMNPQRSTVWXY??????????"
static const char	gCodonNames [] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF"
static const Word	gCursedWord = 1<<31
static MakeIntoWord	makeBase (gBaseBits, gBaseNames)
static MakeIntoWord	makeWord (gBaseBits, gBaseNames)
static MakeIntoWord	makeResidue (gResidueBits, gResidueNames)

---

Define Documentation

#define DEBUG_L1

(

X

)

Definition at line 51 of file GlobalDefinitions.h.

#define DEBUG_L2

(

X

)

Definition at line 50 of file GlobalDefinitions.h.

Referenced by MatchStoreImp::addMatch(), SequenceReaderFile::computeNumSequencesInFile(), MatchAlgorithmUngapped::generateMatches(), SequenceReaderFile::getLastSequenceName(), SequenceReaderMulti::getNextSequence(), SequenceReaderFastq::getNextSequence(), SequenceReaderFile::getNextSequence(), SequenceReaderMulti::getSequence(), SequenceReaderFile::getSequence(), SequenceReaderFile::printSideInfo(), and SequenceReaderFile::printSource().

#define DEBUG_L3

(

X

)

Definition at line 49 of file GlobalDefinitions.h.

Referenced by SequenceReaderMulti::findReader(), SequenceReaderModeFlagReplace::mismatch(), SequenceReaderModeReportReplace::mismatch(), SequenceReaderModeReplace::mismatch(), SequenceReaderModeReport::mismatch(), SequenceReaderModeIgnore::mismatch(), and SequenceReaderFile::printName().

---

Typedef Documentation

typedef HitListVector HitList

Definition at line 386 of file GlobalDefinitions.h.

typedef printBase printWord

Definition at line 630 of file GlobalDefinitions.h.

typedef unsigned int SequenceNumber

Definition at line 250 of file GlobalDefinitions.h.

typedef int SequenceOffset

Definition at line 251 of file GlobalDefinitions.h.

typedef unsigned char uchar

Definition at line 146 of file GlobalDefinitions.h.

typedef unsigned short ushort

Definition at line 147 of file GlobalDefinitions.h.

typedef unsigned int Word

Definition at line 128 of file GlobalDefinitions.h.

typedef WordSequence::iterator WordSequenceIterator

Definition at line 244 of file GlobalDefinitions.h.

typedef WordSequence::reverse_iterator WordSequenceReverseIterator

Definition at line 245 of file GlobalDefinitions.h.

---

Enumeration Type Documentation

anonymous enum

Enumerator:

gBaseBits
gResidueBits
gBasesPerCodon
gCodonBits
gBitsPerWord
gMaxBasesPerWord
gNumReadingFrames
gNumDirections
gNumCodonEncodings

Definition at line 150 of file GlobalDefinitions.h.

{
  gBaseBits = 2,
  gResidueBits = 5,
  gBasesPerCodon = 3,
  gCodonBits = gBaseBits*gBasesPerCodon,
  gBitsPerWord = 8*sizeof(Word),
  gMaxBasesPerWord = gBitsPerWord / gBaseBits,
  gNumReadingFrames = 3, 
  gNumDirections = 2,
  gNumCodonEncodings = 22 
  // = 20 amino acids + 1 stop codon + selenocysteine = 22
  // now 20 amino acids + stop codon + X - TC 27.3.2
};

enum HitListFormatType

Enumerator:

gStandard
g32BitPacked
g32BitPackedProtein
gTranslated
gHybrid
gNotSpecified

Definition at line 172 of file GlobalDefinitions.h.

{
  gStandard = 0,
  g32BitPacked = 1,
  g32BitPackedProtein =2,
  gTranslated = 3,
  gHybrid = 4,
  gNotSpecified = 5
};

enum SourceDataType

Enumerator:

gDNAData
gProteinData
gUnknownData

Definition at line 165 of file GlobalDefinitions.h.

{
  gDNAData = 0,
  gProteinData = 1,
  gUnknownData = 2
};

---

Function Documentation

char* getTimeNow

(

void

)

Definition at line 41 of file GlobalDefinitions.cpp.

Referenced by main(), and processQuery().

{
  time_t now = time(NULL);
  tm* ptime = localtime(&now);
  return asctime(ptime);
}

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void loadFromFile	(	const string &	fileName,
		const char *	buffer,
		const unsigned long	numBytes,
		ostream &	monitoringStream_ = cerr
	)

Definition at line 236 of file GlobalDefinitions.cpp.

Referenced by AllocatorLocal< PositionInDatabase >::load(), HashTableGeneric::loadHashTable(), HashTableTranslated::loadHashTable(), and HashTablePacked::loadHitList().

{


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

    inFile.read( buffer, numBytes );  

    if (inFile.gcount() != numBytes)
    {
      monitoringStream_ << "Error: expecting " << numBytes  
                        << " bytes, but only " << inFile.gcount()
                        << "were read.\n";
      throw SSAHAException("Insufficient data in file.");
    }

    // check for EOF
    if (inFile.peek()!=EOF)
    {
      monitoringStream_ << "Error: expecting " << numBytes  
                        << " bytes, but more were found in file.\n";
      throw SSAHAException("Too much data in file.");
    }


    monitoringStream_ << "Loaded file " << fileName << " (" 
                      << numBytes
                      << " bytes).\n";

    monitoringStream_ << "Closing file " << fileName << "\n";
    inFile.close();

} // ~loadFromFile

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void reverseComplement	(	const WordSequence &	seq,
		WordSequence &	revComp,
		int	wordLength
	)

Definition at line 181 of file GlobalDefinitions.cpp.

References gBaseBits, WordSequence::getNumBasesInLast(), reverseComplement(), WordSequence::setNumBasesInLast(), and shiftSequence().

{
  //  assert(numBasesInLast==seq.getNumBasesInLast());
  for ( WordSequence::const_reverse_iterator thisWord( seq.rbegin() ); 
        thisWord != seq.rend();
        thisWord ++ )
  {
    revComp.push_back( reverseComplement( *thisWord, wordLength ) );
  } // ~for
  shiftSequence( revComp, gBaseBits, wordLength, 
                 wordLength - seq.getNumBasesInLast() );

  revComp.setNumBasesInLast(seq.getNumBasesInLast());
} // ~reverseComplement( WordSequence& ...

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Word reverseComplement	(	Word	word,
		int	wordLength
	)

Definition at line 163 of file GlobalDefinitions.cpp.

  {
    Word revComp( 0 ), mask( 0x3 );
    const int lim ( ( wordLength - 1 )*2 );
    for ( int i( 0 ) ; i <= lim ; i+=2 )
    {  
      revComp |= (((word & mask)^mask) >> i) << lim - i;
      mask <<= 2;
    } // ~for
    //    revComp |= gCursedWord * ((word&gCursedWord)!=(Word)0);
    return revComp;
  } // ~reverseComplement( Word ) const

void saveToFile	(	const string &	fileName,
		const char *	buffer,
		const unsigned long	numBytes,
		ostream &	monitoringStream_ = cerr
	)

Definition at line 279 of file GlobalDefinitions.cpp.

Referenced by AllocatorLocal< PositionInDatabase >::save(), HashTableGeneric::saveHashTable(), and HashTablePacked::saveHitList().

{

    ofstreamSSAHA outFile( fileName.c_str() );
    
    outFile.write( buffer, numBytes );

    if ( outFile.fail() )
    {
      monitoringStream_ << "Error: failed to write " 
                        << fileName << ", aborting save." << endl;
      throw SSAHAException((string)"Problem saving file " + fileName);
    } // ~if

    monitoringStream_ << "Saved file " << fileName << "." << endl;

    outFile.close();

} // ~saveToFile

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void shiftSequence	(	WordSequence &	sequence,
		int	bitsPerSymbol,
		int	wordLength,
		int	i = 1
	)

Definition at line 212 of file GlobalDefinitions.cpp.

Referenced by main(), HashTable::matchSequenceStandard(), HashTablePacked::matchSequenceStandard(), reverseComplement(), shiftSequenceDNA(), shiftSequenceProtein(), and WordSequenceShifted::WordSequenceShifted().

  {
    if ( sequence.size() < 1 ) return;

    register Word oldCarry(0), thisWord; 
    register int shiftNum( bitsPerSymbol * (wordLength - i) );
    register Word carryMask
    (    ( ( (unsigned long long)1 << (bitsPerSymbol*i) ) - 1 )  << shiftNum    );

    register Word andMask( ( (unsigned long long)1 << ( bitsPerSymbol * wordLength ) ) - 1 );

    for (int j(sequence.size()-1); j>= 0; j--)
    {
      thisWord = sequence[j];
      sequence[j] 
        = ( ( ( thisWord << (bitsPerSymbol*i) ) & andMask ) | oldCarry );
         oldCarry = (thisWord & carryMask) >> shiftNum ;
      //      oldCarry = ((thisWord & carryMask) >> shiftNum )
      //        | (gCursedWord * ( (thisWord & gCursedWord) != (Word)0 ));
    } // ~for

  } // ~shiftSequence( WordSequence& sequence ) 

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void shiftSequenceDNA	(	WordSequence &	sequence,
		int	wordLength,
		int	i = 1
	)			[inline]

Definition at line 697 of file GlobalDefinitions.h.

References gBaseBits, and shiftSequence().

{ 
  shiftSequence( sequence, gBaseBits, wordLength, i ); 
}

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void shiftSequenceProtein	(	WordSequence &	sequence,
		int	wordLength,
		int	i = 1
	)			[inline]

Definition at line 706 of file GlobalDefinitions.h.

References gResidueBits, and shiftSequence().

{ 
  shiftSequence( sequence, gResidueBits, wordLength, i ); 
}

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---

Variable Documentation

const char gBaseNames[] = "ACGT" [static]

Definition at line 92 of file GlobalDefinitions.h.

Referenced by main(), and HashTableGeneric::printHashStats().

const char gCodonNames[] = "KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF" [static]

Definition at line 126 of file GlobalDefinitions.h.

Referenced by main(), and operator<<().

const Word gCursedWord = 1<<31 [static]

Definition at line 144 of file GlobalDefinitions.h.

Referenced by codonizeAndFlag(), codonizeAndFlagReverse(), HashTablePacked::countWords(), HashTable::countWords(), getCodonFromWord(), HashTablePacked::hashWords(), HashTable::hashWords(), main(), HashTableView< PositionInDatabase, HashTable >::matchWord(), HashTablePacked::matchWordSubstitute(), SequenceReaderModeFlagReplace::mismatch(), SequenceAdapterWithOverlap::operator[](), and SequenceEncoder::unlinkSeq().

const char gResidueNames[] = "*ACDEFGHIKLMNPQRSTVWXY??????????" [static]

Definition at line 96 of file GlobalDefinitions.h.

Referenced by MatchAlignerTranslated::codonize(), MatchAlignerTranslated::getCodon(), main(), and HashTableGeneric::printHashStats().

MakeIntoWord makeBase(gBaseBits, gBaseNames) [static]

Referenced by main().

MakeIntoWord makeResidue(gResidueBits, gResidueNames) [static]

Referenced by main().

MakeIntoWord makeWord(gBaseBits, gBaseNames) [static]

Referenced by main().

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